Yes it makes sense to parallel your 2 deep cycles and wire a separate starter battery to the other switch position.
The 1/2/both/off switch you have is fine.
The alternator can be set up to charge both banks in several ways, some better than others.
1. Wire the alternator output to the common on the switch. This is what most builders do and has several issues as it puts the control of which battery is being charged on you. You have to be in both to charge both banks. If you forget and leave it on both you will discharge both banks. If you or a guest turns it to off while the engine is running you will likely blow diodes in the alt.
2. Wire the alternator direct to the house bank - the bank most in need. An ACR SI-Series Automatic Charging Relay*—*Blue Sea Systems
or an Echo Charge Battery Chargers | Auxiliary Battery Charger | Xantrex
can be purchased and installed easily which will automatically charge the start battery. The switch becomes for use not charging and errors cannot be made. By far the best method.
Your TrueCharge charger will charge multiple banks. If using an ACR or Echo Charge I would wire it as a single output to the house bank - the above devices will take care of the start battery.
The solar controller or any other charge sources such as a wind gen can be added, their output going to the house bank.