Kim G at Solid Cactus support walked me through this on 2009-11-16.

  To change header banners for the QCO pages to be separate from the
  Sita Sings the Blues Merchandise empire (which uses
  qcsitastoretemplate), here's what Kim said to:

  In store editor, go to Variables (it's the same no matter what page
  you come from), go down to header-background-image, see the sita
  image, click "None" to remove it.

  Now upload the new image (the QCO qcc header image) there.

  Then back go to the top of the Variables page (you should still be
  there) and click the silver "Define New Variable" button.

  Give it name "qcc-sita-header-background-image" and type 'image'.
  Hit Continue.

  You are returned to Variables page.  Look for that new image
  property (should be in the Custom Variables section in the bottom of
  the page).  Upload the Sita header image there.

  Now click the Update button (lower left).

  Now we're going to add a new property to all pages, toggles yes/no
  about which image to use.

  Back at home page, click on "Types" in toolbar.  At bottom of
  resulting page, see Custom Types (should be one or two: we had
  "item." and "print-on-demand".

  (In Store Editor Yahoo calls them "types", but catalog manager calls
  them "tables".)

  Click on "item." first.  See blank edit page, with lots of
  properties and empty fields.  Click on "Define New" on the top.
  Give it the name "qcc-use-sita-style" and set type to 'yes-no',
  check the "Make this new property available in Catalog Manager"
  checkbox, then click Continue.  On the next page, make sure the new
  type is available at the bottom, and hit Update there too.  (Then go
  through that whole rigmarole for "print-on-demand" type too.)

  Now go to "Contents" at the top.  See "css-base" under "sita", click
  on "css-base".  (This is all on a weird-looking template page.)

  THAT WILL TAKE YOU TO A SCARY CSS PAGE!  Don't be afraid.  Scroll
  down until you see buttons.  Click on "Edit".

  Now you're on a style edit box.  Copy the *entire* text in the big
  css box.  Cancel away from this page, and then scroll down again and
  click "Contents" again, to take us back to the contents tree.

  Click the lone "New" button at the top.

  Create "qcc-sita-css-base" and choose "css." as the type.
  Click Continue.

  Paste all that text into the box.  EDIT the css text so it says
  "$qcc-sita-header-background-image" instead of 
  "$header-background-image", and save by clicking Update.

  Scroll down again and click "Contents" to go to the Contents Tree.

  Click on "Index" for the home page.  See the new header banner on
  the home page.  Click on a Sita page (e.g., DVDs), and click on
  Qcsitastoretemplate on the front.

  Now you're on a template page.  Search for "BODY", and two lines
  above that is something like "CALL :yhst-20024741711964-css" with a
  red bar next to it.  (The red bar means 'calling another template'.
  When the red bar is absent, that means that the CALL is calling a
  template that isn't valid yet -- it's not "there".)

  Now we're going to do some RTML!

  Click the yellow "New" button in the otherwise gray bar.

  In the select dropdown, type "if" to get on the "IF" conditional,
  and click Create at the top to create an IF (leaving the "Simple"
  textfield blank at the top).

  The resultant page has an in-progress IF construct at the bottom.
  Ignore it for now.  Click on the word "LINK" at the top, the one
  that applies to "css-base.css".  Now the top gray bar has lit up --
  click the button that says "Replace".

  Now the top has the blank IF construct, and the old LINK is
  out-of-band at the bottom.  At the top, click the "nil" next to
  "then" (the second "nil").  It becomes bold to indicate it is
  selected.  Click "Replace" again.  LINK is selected now.  Click
  "Copy" to copy it.  Now we're going to replace the "nil" that's next
  to "else".  Hit "Replace" again to take the LINK that's now at the
  bottom and replace that "else" clause.

  Now the "else" LINK should be selected.  Click "Edit" at the top.
  Change the name of the href to "qcc-sita-css-base.css", leave Add
  blank, and hit Update.  The else LINK will still be selected.

  Now we have to replace the IF test.  Click on the "IF" (*not* on the
  "nil" next to it).  Click "Edit" button, enter "@qcc-use-sita-style",
  and hit Update.

  Now on the RTML page, look at the first row of buttons.  The last
  button always says the name of the page you were on when you started
  editing the template.  Right now it says "DVDs".  Click on it to go
  to that page in the store editor.

  *** Oddly, it still had the sita store banner.  I hit Cancel from
      the Edit page to go back to the DVDs page, then hit reload there
      to see if the banner refreshed to the new QCO banner.  It stayed
      the old banner, as did the home page, even though the templates
      were correct.  At this point, we were mystified.  I gave Kim
      access herself: solidcactus_saas / kimg@solidcactus.com, with
      the Store Editor role. ***

  AHA!  She discovered our 'then' and 'else' clauses were reversed.
  We went back in to fix that:

  From home page, click on the qcstoretemplate button.  Search again
  for "BODY", two lines above is the CALL of the css, click on the red
  bar again.  Click on the "LINK" before "else", then once LINK is
  selected, "Edit" from the top bar.  Copy the value there, then edit
  it to make it the old "css-base.css" value.  Click Update.  Click on
  the other LINK; click "Edit"; put the copied new css value into the
  css box, and hit Update.

  Click on "Index" at the top to go back to home page.  Go to DVDs
  page; click "Edit" at the top.  Scroll down to the bottom, and
  toggle the Qcc-use-sita-style property to "Yes".  Hit Update.

  Do the same for every page (including item pages) that need it.

  Each page (including item pages) also has a page title.  Just edit
  those as desired.  Most item pages already have an appropriate title
  for their content, and won't need to be edited.

  NOTE: the sita.html page is a different type than other pages, so it
  didn't get the qcc-use-sita-style new property that we created
  earlier.  So, create it now under Define New, as a yes-no.

  When make a new better QCO banner, go to Variables and upload it as
  header-background-image.

  The only thing left now is to toggle the yes-no var on all item
  pages that need the Sita banner.  But that's a lot of pages.  So we
  went to catalog manager.  From a Store Editor page, click "Manager"
  on the top tool bar, and go to Catalog Manager.  Go to "Manage Your
  Items".

  In the narrow white horiz bar, click on "Customize View" over on the
  right.  "Add" qcc-use-sita-style over from the left to right side.
  Now it's displayed as a column, back in Catalog Manager.  Now click
  the "Edit These Items" button, toggle what you need, click "Save".
  Back in Catalog Manager, choose "print-on-demand" from the dropdown
  on the left (where it used to say "default tables", and repeat the
  process for all the POD items.