Templating (or themes, as Moodle normally calls it) is very different between Moodle 1.9 and 2.0. Hopefully the new system in Moodle 2.0 is much more flexible and easier to work with.
However, I expect that if you did develop for 1.9 first, quite a lot of your CSS would still work in Moodle 2.0, after you had moved it to the right place, however, that is a bit of a guess.
Testing and QA
Developing in moodle 2.0 or 1.9.9+
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