I recently purchased 2 mppt epever charge controllers and i noticed one was negative and the other positive common. What is the main differences and is it possible to hook these up in parallel to the same battery and inverter.
If you mean connect the same solar panels and batteries to these unit, then no, you can't hook them up in parallel.
Basically what will happen is the Pos and Neg from the solar panels will feed straight through w/o any regulation. That is, if it doesn't blow up the devices.
If you take a continuity tester (beep/diode mode on an multimeter) and probe the Neg leg on the Neg common unit, there'll be direct connection. Same if you prob the Pos leg on the Pos common unit.
If you mean that they have different panels input, and connect to the same battery, this would be fine. AS LONG AS you never ever connect the grounds/negatives together on the panels between the two units. Which, this is unlikely if these are roof mounted units. If they are field mounted, then you can keep them separated.
Roof mounted systems are tied to ground for lightning protection. So you wouldn't be able to isolate them easily. Ground mounted you can have completely separate grounding systems.