That depends on how sporty you are. The patcher allows you to make a copy of your sh5.exe file (the core executable file of the game), make changes to the copy with the patcher, and then install the patched sh5.exe just like any other mod. When you activate this or any mod with JSGME, JSGME saves a copy of the file being overwritten, and restores that file when you deactivate the mod.
You CAN point the patcher at your primary sh5.exe file and patch IT in place. But remember that you are making changes to the code you paid the forty bucks for. Programmers consider this high-risk behavior. (Tells you how dull programmers' lives are!
) The important point is that the patcher is designed and intended to let you easily avoid modifying your primary .exe file. I prefer to use it that way. YMMV.
Whatever you decide to do, I suggest you read this before you try to use the patcher.
http://www.subsim.com/radioroom/showthread.php?t=197960