jdMorgan - 12:52 am on May 28, 2011 (gmt 0)
Your root-level .htaccess containing the domain redirect will execute first and pre-empt the .htaccess file in the WP subdirectory. All you'll need to do with the WP .htaccess code is to make sure that any redirects that it contains refer to the proper (new) domain instead of the old one.
You should know that "moving" an entire site may knock you out of the search listings from anywhere from a few days to several months -- more likely the few days. Changing domains on a revenue-producing site unless absolutely required (say, due to a court order) is a Bad Idea (TM). Try to get several of the most-important (i.e. both relevant AND high-ranking) sites that link to you to update their links to refer to the new domain as quickly as possible to mitigate this. However, things should settle down and return to normal once the major SEs have re-indexed the majority of your site with its new domain name.
If you're having some problem with your code, then please post the code and identify the specific problem to get more useful answers.