I'd suggest that the optimal setup where space is limited would be two "Dual Purpose" type batteries. That way there would be plenty of CCAs in either batery to start the engine, and nearly as many amp hours in reserve as one would have with a pair of "deep cycles" .... and I believe you'd get more longevity than with a pair of deep cycles which had been subjected to starting use. At least that's what the tech advisors told me at Decca Battery which is located near where I used to live.
Did the tech bother to ask you how many cranking amps you engine actually required? Sure, if you have a 3208 Caterpiller you might need 700 cranking amps but with a small aux diesel you don't!
For example my 44HP 4 cylinder Westerbeke has a max rated cranking amp draw of 160 amps. In the real world, as measured by my Xantrex XBM, she's never pulled more than 100 amps to actually start my engine. Even the smallest personal water craft battery has more than 100 CCA!
People often over estimate the amount of load or amp use caused by engine starting. I can start my engine and not even measure 1 tenth of an amp hour used.
Standard deep cycle batteries will last longer and also will start any sailboat aux engine in the 30-50 foot range. Using start batteries or dual purpose batteries is 100% unnecessary with small aux engines unless you need to save money. I have not owned a start type battery in over 10+ years...
Here are two photos I took the first is prior to starting, after a night on the hook, the second is immediately following engine start. As you can see the amp hours required to start my 44hp diesel were not even measurable...
Immediately after start: