Sigo, since you are wiring the aux battery from scratch, I presume you are free to mount the battery with the positive terminal to the left or right, and would be able to adequately run the wiring either way. If this is true, then I would mount the battery whichever way gives you the most clearance from the positive terminal and body ground. So on one side you have the fender, and on the other, you have the radiator. If it doesn't cause any wiring complexities, I would install the battery whichever way give the most clearance between the positive terminal and a body ground (fender or radiator).
With respect to which Blue Sea solenoid to select, one major difference between the automatic and manual solenoid is that the automatic solenoid has built in to it the concept of a "primary" battery. It will always first fully charge the primary battery, and only after the primary battery is charged will it begin to charge the secondary battery. So this will work fine as long as your setup indeed has a primary battery. Many dual battery systems have one battery for starting and a second battery for aux loads, in which case the automatic solenoid may work well, with the starting battery being the primary battery.
For the system I will be installing, neither battery will be “primary” (as either battery, either singularly or in combination, will be able to supply all loads), therefore the automatic solenoid is not suitable for me.