Actually if it was the manual transmission it would matter. There aren't provisions on the cherokee manuals transmissions to wire for a neutral safety switch that the AW4 autos have. The circuit could be bypassed on manuals(I have done it to mine). This is a major safety issue and I highly recommend not wiring a remote start in a manual vehicle unless there was that neutral circuit. I have since removed my remote start system and will be installing it into my AW4 equipped XJ.
I have attempted to start the jeep with it in gear and it quickly becomes a self propelled rocket. Luckily no one was injured and only damaged a brand new, temp tag still on, Kia. Damn foreign plastic cars!!! anyway. My wife did the same thing as well with it and hit an explorer. Again no one was injured. I quickly yanked the system.
As far as brands, the one I removed and the one in my wifes Suburban are both Crimestopper. I have been extremely pleased with both units, and with those you can program one key fob to control both vehicle starters independently.
HTH