These instructions are actually more specific to the G15, where the MR button has macro recording functionality built into it if you have the profiler running. Disabling the profiler is also useful for preventing issues related to the software automatically switching profiles depending on the active application.

So here's the answer as far as what you want to do with the G13.

You absolutely positively can leave the logitech software running. You don't even need to clear the profile. Clearing the profile prevents double-binding and ensures that the user is aware that there are default bindings on the device (otherwise the keys on a G15 for example will press 1-6, F1-F6, etc). IS will detect the button with or without clearing. You can bind to each button in either software, or even both (not recommended). I helped a few people before that run the profiler just for the thumb stick on their G13.

The other thing is that if you're running Vista or Windows 7, you will need to run the profiler as administrator (or have UAC disabled).