There's an infinite number of ways to go about this 
When you use ISBoxer, it becomes less about "is it possible to _____" and more about the way you want things to work -- so if the following isn't what you want, you tell me what you want to happen when you push a particular button 
Here is a hotkey that can toggle auto-assisting on/off, assuming you are using ISBoxer 38.2.329.1 or later:
Code:
<?xml version="1.0" encoding="utf-8"?>
<Box xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
<ObjectType>ISBoxer_Toolkit.Configs.KeyMaps.MappedKey</ObjectType>
<SerializedObject><?xml version="1.0" encoding="utf-8"?>
<MappedKey xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
<Name>Toggle auto-assist</Name>
<Description />
<SendNextClickBlockLocal>false</SendNextClickBlockLocal>
<ManualLoad>false</ManualLoad>
<ResetTimer>0.1</ResetTimer>
<ResetType>Never</ResetType>
<Mode>OnRelease</Mode>
<Steps>
<Step>
<Stick>0</Stick>
<Stop>false</Stop>
<Actions>
<MappedKeyAction xsi:type="MappedKeyRewriteAction">
<Target>all</Target>
<FromMappedKey>
<KeyMapString>General</KeyMapString>
<MappedKeyString>FTL Assist Me</MappedKeyString>
</FromMappedKey>
<ToMappedKey />
</MappedKeyAction>
<MappedKeyAction xsi:type="MappedKeyStepAction">
<Target>all</Target>
<MappedKey>
<KeyMapString>General</KeyMapString>
<MappedKeyString>Toggle auto-assist</MappedKeyString>
</MappedKey>
<Action>Set</Action>
<Value>2</Value>
</MappedKeyAction>
</Actions>
</Step>
<Step>
<Stick>0</Stick>
<Stop>false</Stop>
<Actions>
<MappedKeyAction xsi:type="MappedKeyRewriteAction">
<Target>all</Target>
<FromMappedKey>
<KeyMapString>General</KeyMapString>
<MappedKeyString>FTL Assist Me</MappedKeyString>
</FromMappedKey>
<ToMappedKey>
<KeyMapString>General</KeyMapString>
<MappedKeyString>FTL Assist Me</MappedKeyString>
</ToMappedKey>
</MappedKeyAction>
<MappedKeyAction xsi:type="MappedKeyStepAction">
<Target>all</Target>
<MappedKey>
<KeyMapString>General</KeyMapString>
<MappedKeyString>Toggle auto-assist</MappedKeyString>
</MappedKey>
<Action>Set</Action>
<Value>1</Value>
</MappedKeyAction>
</Actions>
</Step>
</Steps>
</MappedKey></SerializedObject>
</Box>
This page http://isboxer.com/wiki/ISBoxer_Releases will tell you how to make sure you're on that version or later (there will likely be a pushed update this weekend anyway).
Anyway, if you copy all of what's in that code box including the first < and the last >, you can then paste it into the General key map in ISBoxer and give it a Hotkey. To do this:
1. Copy the XML code as described (all of it)
2. In the top pane under Key Maps, select General
3. In the bottom left pane right click on Mapped Keys, and select Paste Mapped Key from Clipboard. If you do not see this option you are either not right clicking on Mapped Keys or do not have it copied to the clipboard.
4. In the bottom left pane select 'Toggle auto-assist' which we just added
5. In the bottom right pane at the top is a Hotkey option, click the < and set it to your new toggle key.
What this key does, is set it up so that when FTL Assist Me is used as part of another Mapped Key (like your DPS keys) it can be disabled. Using the FTL Assist Me HOTKEY (alt+backspace by default, can be whatever you want) will still make your guys assist.
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