thats the order i would do them if u are still having problems.
do the big 3 in 1/0, followed by possibly replacing your starter battery and/or adding a ceep cycle in the back or 2, followed by adding a single or dual alternator setup depending on how big of a system we are talking.
If I were to get an extra battery would I also need to get a bigger alt. to charge both batteries. When I had my truck I had 3 batteries total and I never upgraded the alternator and I had all sorts of problems. I'm not sure how many amps the alternator in my 2006 Suzuki Grand Vitara pulls, but I believe I'll have to upgrade my electrical in order to strap 2 Power Acoustik A2400DB's and my component amp. And I don't have much money to work with.
step back and evaluate what you are working with. If you are running a lot of power...get an HO alt. Don't mess with adding batteries...First you have to be able to supply the current.