Effect of Battery charging with un equal batteries in parallel
Even parallel charging expensive batteries of the same type is unwise. If you are using deep-cycle batteries then they almost certainly justify using a charger that can manage each independently or separate chargers. 

During UPS operation you want the combined energy of all batteries (of course). If these have all been floated and are fully charged then you can "with reasonable safety" combine them at this stage. 

Best/nicest would be to have the ability to stagger discharge and apply each new battery as desired. 

Either of the above schemes ideally requires the ability to zero or close to zero voltage drop connect the batteries to load. Traditionally this would be done with contactors but can be done with modern MOSFETS at low loss and quite reasonable price. 

For example, this utter gem of modern technology Infineon N-Channel MOSFET IPB009N03L at $3.44 /1 in stock at digikey is rated at 30V, 180A, Rdson &lt; 0.001 ohm [!!!!] 0.6k/W Tjc. 

At 30A with a wisp of copper it would be warm.
 At 100A it would need sensible heatsinking.
 I do not know the sensible design current or the package (as opposed to the device ratings) but the package seems to be trying harder than some to deal with the current. A few of these or something similar could well allow you ease of charge-separately, "connect as required" operation.