It sounds like you will definitely be upgrading the amount of panel you have and connectivity is at question. If you use a combiner box on the roof, it will all be a lot easier, no matter which wiring schedule you choose. The combiner box can offer easy termination of parallel sources and can also be used for a series string.
Since I'm a miser about lost voltage and I already had a spool of 4 AWG , I used that from the combiner box to the controller. I only have one module, at present, but can easily add more, if needed. Like Niner says, initial tally of how much power used in a typical day (along with some headroom) is a good starting point.
At some point, you may want to think about multiple higher voltage modules. There's some cost and ease of use benefits with the bigger modules. The layout of your roof will dictate, sometimes, what you can fit. The higher voltage panels will also mean MPPT controller, only.
FWIW, I have a Morningstar controller and it is quite a sophisticated device for the price. It allows a user to tailor charge settings, duration, equalization, and is temp compensated. It also has a PC interface so data logging, graphs, etc. can be made and saved. Lots of geekiness.
Good luck with your upgrade.