I think the key with this (excuse the pun), will be to make sure to run all of it through the cycle covering all keys.  For me, it seems to be the only way to get full command over things on the guitar, so I can actually use them without having to think about it.  I don't want to have to think so much when playing, but rather listen.  I'll let you know how it's working for me as well as what I'm struggling with.