If you followed the instructions, you should no longer have an aquaria.exe file on your desktop, since that file would have been moved into your Aquaria folder. Once you are done patching, you can run Aquaria the same way as normal, by selecting it from the Start menu. If it works, you can delete the aquaria-backup.exe file from the Aquaria folder. If it doesn't, you can at least get back to the way it was before by deleting the aquaria.exe file and renaming the aquaria-backup.exe file back to aquaria.exe.
If you're concerned that you might have messed something up, you can always save a copy your save game files (found at c:\program files\aquaria\save, except in
Windows Vista), then uninstall and reinstall Aquaria. Then try the patch again and copy your save game files back into the save folder.
At this point, if you aren't able to get it working, Alec or Derek will have to help you. I don't have anything to do with Bit Blot.
Alec and Derek, maybe the upcoming 1.1 patch could come in the form of an EXE that will locate and patch the game for you, instead of relying on the user to drop the files in the right place themselves. While the instructions for the patch seemed pretty straightforward to me, an EXE that would just do it for you would prevent anyone from having the problem in the first place.