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i think you should keep them both hooked together, the starting battery can handle the higher discharge rate that the starter motor draws so as the starter cranks over it's voltage is going to stay higher but the deep cycle battery should have more bulk capacity to it to sustain electrical needs, working together you get the greatest capacity as well.
If you wanted tho, you could just hook the starting battery to the starter and the deep cycle battery to the rest of the car electrical and use an isolation diode to allow the deep cycle battery to bump that voltage of the starter battery back up after starting, it would also allow it to "help out" a little with starting, that way the starter will always be sure to start even if you leave your lights on and a simple jumper wire would allow you to get home, auto part stores sell isolation diodes for RV's.
As for charging, if you have them in parallel you are fine to charge them together, 1.5 amps is a slow charge rate, small starter batteries tend to be around 40 amp hours and 120amp hours is not uncommon in larger engines and deep cycle batteries tend to be 100 amp hours on up to 225 amp hours, so if you are draining these batteries down, you could have 140 and up to over 350 amp hours of battery that you are trying to charge, at 350 amp hours you could pretty much leave that 1.5 amp battery charger on for weeks without worry of over charging and they tend to taper off as the battery gets full so it's rare that it's ever a full 1.5 amps unless the battery is dead, a good idea is to get your your volt meter and see what the battery voltage is after you pull the charger off the batteries, make sure you are getting them charged up all the way or you will kill your batteries early, for this reason I like higher amp battery chargers that either float or shut off when full, there are some nice weather tight ones that you can mount right on the car.
Other thing is, if you want both batteries to get the full advantage of the charger, hook the positive of the charger up to the positive on one of the batteries and the negative up to the negative on the 2nd battery, that way a bad connection between the batteries don't leave one lagging behind for an early death.
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