We have MPPT controllers on both boats, one with 200 watts and the other with 480 watts. I'd normally recommend them but in your case maybe not unless you had quite a bit of money
to spend on them. Notice the "them".
Our panels on both boats really aren't subject to shading or if so very little for maybe a very short time of the day. If you have read some of the other threads here and elsewhere on shading you can see it can significantly reduce power and yes wiring in parallel will help to reduce that but still not eliminate it.
In your case where you know you are going to get shading maybe break the array down into 3 separate arrays. One is off the stern with very little if any shading and the other two are the ones that get shade. Hopefully one will be in shade and one won't.
Buy 3 PWM controllers and use one for each array. 3 of them will be about the same price
as one MPPT. Now hopefully at least 2 of the arrays will be producing most of the time.
3 MPPT controllers would be better yet if you could afford them, but if not I think the 3 PWM controllers would out produce the 1 MPPT controller if some of the panels are in shade.
Morningstar has some nice PWM controllers and the 10 amp are about $45 and the 20 amp about $77. Use two of the 10 amp for the shaded panels (2) for each controller (4 total) and the 20 amp for 4 panels on the back for a total of $167.
If you went the MPPT route
you could get something like a Blue Sky 2512i for around $180. We have one of those on our smaller boat. They are rated to 25 amps, so you would have to see what those panels are putting out and you might have that controller maxed out (there again I'd call them).
Once again normally I'd recommend and use the MPPT, but in this case the 3 PWM controllers might be the best deal. If money
is available you could replace all with MPPT or maybe the one with the 4 stern panels.
I talked to a tech the other day at Blue Sky Energy and they recommended breaking an array up with multiple controllers if you knew you were going to get shading.
Blue Sky Energy Inc. - Industry Leaders In Solar Boost Charge Controllers and Maximum Power Point Tracking (MPPT)
Call them and talk to them about your situation or call one of the other manufactures of quality controllers.
Personally I'd just try and permanently mount all the panels. You will soon tire of trying to move them around and then you also have the wiring to deal with doing that.