Keeping changes compatible with new versions

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Hi,

I'm new to oscommerce. I'm just starting to look at building a site on the CVS version. A problem I'm finding is that I need quite a different look and feel, additional database tables
for complex product types etc, and that the changes I'm having to make to the test site are scattered all over a lot of different php files - it's very difficult to keep them self-contained.
But when I'm done I'd like to be able to upgrade to new versions without a huge amount of
work.

Is that impossible? Does anyone else have any good ways of achieving this? Or is the only way a lot of fiddling with diffs and patch files? Or do people who make big changes to oscommerce just freeze it at whatever version they started from? 

Sorry for such a general question... Any advice appreciated :-)
Graham