Xvoltswitch

I'm new to the forums, but I am having this problem using wrye bash for skyrim. I check all the mods I want to run, then I run the dual sheath redux patch, (or any skyproc patch), after it runs it says I need to add dual sheath redux.esp to load order. when I open wrye bash again, most of my mods are unchecked. Is there a way to make sure the patcher doesn't uncheck my mods? Â -Thanks to anyone who can help :D