For setting up FTL in HotKeyNet, you'll want to use Templates.

http://www.dual-boxing.com/threads/1...with-templates

I really don't have any idea on Jamba's FTL Helper. My {caffine-deprived} understanding is that the FTL Helper in Jamba is a means of creating the in-game macro part. So rather than having to write out a macro that reads like this

Code:
/assist 
[mod:ctrl,mod:shift,nomod:alt]ToonA;
[mod:ctrl,mod:alt,nomod:shift]ToonB;
[mod:alt,mod:shift,nomod:ctrl]ToonC;
[mod:ctrl,mod:alt,mod:shift]ToonD;
[mod:ctrl,nomod:alt,nomod:shift]ToonE
/cast [harm] Lightning Bolt
you'd use the FTL Helper {under Jamba Advanced} to assign the modifiers for your team and write the macro out using the FTLAssist-Button

Code:
/click JambaFTLAssist
/cast [harm] Lightning Bolt