No problem -
If running two batteries.... tie them together, parallel'd. Positive to Positive and negative to negative... As you've stated, you'll have a 1/0 or 1gauge copper (recommended, use the handy wire sizing chart provided in this forum) feed from your alternator, direct back to the battery. From the + of the battery you'll go to one side of your master kill switch... From the other side of the master kill - you'll run to your starter solenoid... and or other critical electrical components from there.
For what it's worth - I have a starter solenoid in the trunk so as not to have a constant hot running up the frame rail ... The big starter wire is only hot during cranking.. and I have it fused at 150amps. I also have the alternator feed to the battery fused at 150amps. One of Rays (moderator, CS130's) ..I run a continuous duty solenoid (200amp).. and use my Painless Switch panel to open and close this solenoid.. from this solenoid.. I feed a Dedenbear Relay Center MRC1... where everything is conveniently fused and relayed. I basically run the whole car off this center...and within fingers reach if something trips.. I have manual resettable breakers in this relay center... It's fed with a #2 Copper cable..
Make sure you ground everything solidly and fuse all your accessories accordingly. You'll be good to go. Good luck.
