Well, you will need to “merge” the existing .htaccess file for WordPress with the appropriate re-write condition/rule changes to facilitate the uber-uploader integration with WordPress (similar to but not exactly like the “stats” example).
Once this is done, if it is done correctly, you may, or may not, need to use the mod-security disablement via .htaccess suggestion re. the uber-uploader flength error. If you do need to do that, you may be able to do that in a separate .htaccess file, depending upon where you installed uber-uploader. Note that you can accomplish the same thing as that uber-uploader .htaccess fix by disabling “extra web security” for your domain from withing the DH web control panel (Domains -> Manage Domains -> Edit (under the web hosting column for your domain). DreamHost’s “Extra Web Security” is mod_security.
Of course, as norm1037 correctly points out, you can avoid having to deal with this at all should you just use a subdomain for your uploader.
That said, there is no reason why you should not be able to use WordPress and uber-uploader together if you have them properly configured, and while it might seem “epic” at the moment, I believe the situation is fixable.
Note that you will likely have to account for the cgi-bin directory as well as the uber-uploader directory in the modified rewrite conditions/rules if you used that in your uber-uploader installation. You do not have to even use a cgi-bin on DreamHost (thanks to suEXEC) but then you will have to modify your installation to indicate ubr_uploader.pl’s actually location.
The first place to start to see what is wrong is your error logs - that “500 Internal Server Error” is notoriously useless, as it doesn’t really give any hints as to what caused the error. Looking at your error logs will often provide more clues - the error could be (and often is) something very simple, such as using an improper editor on a perl script, or having a random character or CF/LF in a file.
What does your error log say when the 500 Internal Server Error is displayed?