Jon,
Congrats on the new reel
I just picked up on of their 300's and I can't wait to break it in. Hopefully, I'll be able to tug on a good sized bass pretty soon. I dunno if it was the right way to rig it but I have 50lb spectra on it with a 20lb topshot, I'll have to see how it works.
For Mission Bay, I used to fish up towards the San Diego Sailing Center complex. The slow zone buoys keep the boats away a bit, plus there is/was a good amount of eel grass there for the bass to hide in. Another place that was producing recently was at the other end in front of Sea World. I like the Franko maps also, in fact I use them quite a bit for scouting different bays and whatnot.
Perry