In LimeWire, go to: Tools > Options > Saving
this will show the path to the folder LimeWire defaults to for saving files. You can change the folder to save to by clicking "Add" and then browse to your normal folder and click apply.

Then go to: Tools > Options > Sharing and see what folder(s) LimeWire is sharing. You can delete folder(s) and add whichever folder(s) you wish.

If you have any files in the default LimeWire saving folder, you can manually move them into your normal folder and delete the LimeWire default folder in Tools > Options...

I personally choose NOT to share the folder that LimeWire saves to. I prefer to test the files before I move them to my shared folder. Don't want to share any "bad" files.

I hope this makes sense. If you have any more questions, please post back.