The next iteration of SCI Companion, combined with the template game, will feature some extra debug functionality which I think will be pretty useful.
Through some file creation magic, you'll be able to start your game in "debug mode" which will enable the DebugPrint function. DebugPrint can be used just like FormatPrint:
DebugPrint("Switching to room %d" newRoomNumber)
So you can sprinkle these in your code when you're trying to track down a problem. This function will write to a file, which is read by SCI Companion, and displayed in the output window (which will now have tabs for Debug Output, Find Results and Compile Results). If the game is not started in debug mode, then DebugPrint just does nothing.
In addition, you will be able close the game (terminate the process) from within SCICompanion.
Not only that, but you'll also be able to "debug a room". Above the script editor will be a button that starts the game and takes you directly to the room for that script. Of course, this also requires support in the template game, and it requires that the room in question is functional without having to go through the title screen, etc...