That depends on what you setup, and how.
If you don't have videofx or repeater regions that you created via the ISBoxer in-game control panel, and you dont have specially saved menu positions, and you don't have custom images setup, then you can fresh install ISBoxer, and only copy your ISboxer Toolkit Profile (File -> Save As in ISBoxer Toolkit), and it will have everything.
You can also just copy the complete Inner Space folder, usually from C:\Program Files (x86)\InnerSpace
This also contains everything. You need to put it back in the same place on the new machine, because when you install it the ISBoxer profiles use some items which are hard coded.
In both cases, you may have some fix up work. Your games should be installed to the same locations they are currently, so when Inner Space references them, they are still found. If they are not, you will need to
Add them to Inner Space again (if they are not autodetected that is), and probably update the Characters in ISBoxer to use the appropriate Game/Game Profile setting.