Putting new binaries into the aquaria main folder should be enough to get it to run (but backup your old ones + usersettings.xml!)
Depending on which version you use, you may have to update your script files as well (for achurch's PSP version). I recommend doing so, as some bugs have been fixed there as well.
There is a few data missing, most noticeable is that achievements (which have been added after 1.1.1) have no name and no text, but apart from that, the game runs well. Not seen other problems so far, but haven't played it through completely with my own build.
If you have problems with AQConfig messing with your settings (like disabling the controls, making aquaria choke and crash), rename it to something else, and edit the user€settings.xml file by hand.
Btw: Mods are not (yet) working with achurch's version. The 1.1.4 version that was mentioned in another post is a rough plan to get order in the chaos, and end the versions/build mess, which is hard to keep track of for casual users.
Its the same on linux.
Hope that answers your questions.