There are various options for using Logic directly in hacking; unfortunately none of them are particularly good ideas.
I'm guessing you mean the "Tweaking the Rules" optional rules from Unwired pg39?
It suggests using Logic to replace program in the hacking test, and then using the program's rating as maximum number of hits. (eg. To crash a program instead of Hacking + Exploit, you roll Hacking + Logic. But if you only have an Exploit 3 program, you can't score over 3 hits.)
Or alternatively, you can reverse it: You still roll Hacking+Exploit, but limit the maximum number of hits to the character's Logic.
Personally, I don't think that second option is that bad and am strongly considering using it as a houserule, figuring the 65IQ guy just wasn't smart enough to come up with the right program parameters. (Spending edge overrides the rule.)
Why's it so bad?