I'd be inclined to record each cassette side as one big lossless file and then deal with splitting the songs after the fact. This does mean that you'll need a "lot" of disk space: 200 cassettes * ~50 min/cassette * 60 sec/min * 44100 samples/sec * 32 bits/sample * 1/8 bytes/bit * 1/1024 kbytes/byte * 1/1024 Mbytes/kbyte * 1/1024 Gbytes/Mbyte ~= 100GB. Less if you use some sort of lossless compression.

But then you have all the data on the computer and you don't have to deal with the cassettes again while you figure out the splitting.