You'll want to install php in the same domain that you want to be able to use the higher upload limit.
I'm not sure what level you're at in regard to techincal know how, you might want to read over the instructions for setting up your own install of php and see if it's all greek and way out of your league, or somehting you think you can handle. It's not exactly beginner material I think.
Anyways, once you get your php installed and working, you can edit the upload in the php.ini file. I think that's covered in the instructions, several people have put in their own version of php to get around the upload limit. Just beware that this could conceivably make your domains less secure, if a script were to get hacked.
Hope this helps