How to deal with this? Should I try and maintain the two separate templates.

With care in defining the templates for the header, left and right columns, it should be possible to "mix n match" those components by concatenating the templates, or concatenating the results of expanding the templates.

Your generating script then looks something like this pseudo-code:

if needsHeader
    load header template
    expand header template
    output expanded header to file
endif

if needsLeftColumn
    load LeftColumn template
    expand LeftColumn template
    output expanded LeftColumn to file
endif

if needsRightColumn
    load needsRightColumn template
    expand needsRightColumn template
    output expanded needsRightColumn to file
endif

...
[download]

This way, you specify your pages at a higher level in terms of the subcomponents that need to appear on the page, and your generation script processes that higher level description by loading and expanding the appropriate mix of templates.

It does require care in defining the subcomponent templates, but with the use of css, and especially css2, it can make for a very concise page specifications, if the nature and layout of the data you are presenting is, or can be, standardised.