I try to start my 1988 Jeep YJ (maunal trans) and I just hear a "click, click" sound. Jump started it and it was running, but I stalled it and the same thing, she wouldn't turn over...just heard the click click noise when I turned the ignition. Is this something to do with the "battery realy"?

First thing to check is the battery on jeep. If the battery is low on power or dead,charge the battery or replace it with a new battery. It sounds like you are not getting enough voltage to the starter to turn it over and start the jeep. Once you get the jeep started use a volt meter to check the voltage at the battery. The alternator should be putting out 14 to 15 volts to the battery. Check the battery cables at the battery,clean and tighten if need be. If the alternator is not putting out the voltage as i described then replace it. Make sure the radio and a/c is turned off in jeep before you run your test. Hope this will help.