The %1% and %2% actually just call the 1st and 2nd value after the assist1 command

So <Assist1 "firstvalue" "secondvalue" will replace any %1% with 'firstvalue' and so on.

In my case the first value is always %trigger% which just fills in which hotkey was pressed to save writting it out each time. For button #1 <assist1 1 t> actually does the same thing.

This is what broke my setup when using a shift + key modifier since it would then read <assist1 shift 1 t> ends up attempting to send only shift to the main window and mods + 1 to the others rather than t. I have got this working fine but is a little messy, I had to create <assistmod> commands to use instead and including a %3% variable.

This explains it better than I can

I'm more than happy for anyone to link this or put it on the wiki, I'll even do it myself if needed :P