You cannot expect any device to function without a battery. Saying you cause problems with the loading of JL_cmd after putting in the battery is something normal. What do you expect the BB to do? You need to read the instructions and try to understand what they are telling you to do.
Here are some links but if you dont read them expect to end up with a rock.
How do I wipe the BlackBerry using Jl Cmder? - BlackBerryFAQ
How to wipe ALL personal data from a BlackBerry device? - BlackBerryFAQ
What to do next if Jl Cmder will not connect and wipe - BlackBerryFAQ
How do I upgrade the OS on my BlackBerry? - BlackBerryFAQ