Feider has been asking me for help with this again recently, so here's the new method (as of today) to set up such a toggle.

ISBoxer 40.2.424.1 added a Mapped Key Wizard to replace Many New Mapped Keys. The new wizard can generate several kinds of Mapped Keys. 40.2.425.1 adds "Key Map Toggler" to the kinds it can do. Key Map Toggler will toggle Key Maps or Mapped Keys of your choosing. In this case, it would have been "FTL Assist Me" in the "General" key map -- by disabling FTL Assist Me temporarily, there would be no auto-assist on the default "DPS 1" through "DPS =" mappings, because they use "FTL Assist Me".

So in order to follow these instructions, make sure you have 40.2.425.1 or later (via Help->About in ISBoxer; there will be an update link in the About window if there is an update for you).

Step by step to do this:
1. In the top left pane, under Key Maps, select Control
2. In the bottom left pane, right click "Mapped Keys" and select "Mapped Key Wizard"
3. When it asks what kind of Mapped Key to make, select "Key Map Toggler"
4. Click Next. Now you see the Key Map Toggler options. It shouldn't be incredibly hard to follow except there is separate boxes for Key Maps/Mapped Keys that should be turned OFF in step 1, and those that should be turned ON in step 1.
5. Set a Name for your toggle. This is required and becomes the name of the Mapped Key. Example: "Auto-Assist Toggle"
6. Configure a Hotkey for your toggle by clicking the <. This is optional; if you know what you're doing you could use this toggle via a Click Bar or Do Mapped Key Action and not need this Hotkey configured.
7. Select a Target for your toggle. This controls which windows toggle the given Key Maps and Mapped Keys. This means Hotkeys will be activated for use from those windows, or de-activated to not be usable from those windows. It also means that Do Mapped Key Actions to use de-activated Key Maps/Mapped Keys will not work until they are re-activated. Most of the time you probably want this Target to be "All w/ Current" in order to apply to all windows.
8. In the center area it says "Add Key Maps and/or Mapped Keys to toggle". Select only a Key Map to add a Key Map, or select both a Key Map and Mapped Key to add a specific Mapped Key. In this case, select Key Map "General" and Mapped Key "FTL Assist Me", and click "Add to OFF" to make it turn OFF for the first press, and therefore ON for the second. If it were off by default you would want to turn it ON first, but it's on by default so you want to turn it OFF first.
9. Optionally, configure Popup Text notices to be shown in Steps 1 and/or 2. If left blank, no Popup Text will be used. Example.. "Auto-Assist OFF" and "Auto-Assist ON"
10. Click Finish
11. Export to Inner Space. Your toggle will work with the given Hotkey.

It looks like a lot of steps but that's because this is the complete idiot breakdown. It's easy. Enjoy