Paralleling different panels with different electrical characteristics to one MPPT controller is not a good idea. That's not the intent here, though. The OP should have no problem connecting the output of the two controllers at the batteries. Both input connections should be fused for the amperage of the wire within a couple of feet of the batteries.
If the separate outputs from the controllers are joined at a midpoint, as BFL suggests, then both outputs should be fused before that junction and the battery termination will also have to be fused. When using "fused" in this post, a guy could also use circuit breakers instead of fuses, the main thing is to circuit protect any wiring.
