How can I correct an irregular problem with how Mail is working?

I am running OS 10.7.5 on an iMac early 2008 20" machine. In the past couple of months my mail program seems to indiscriminately put some unread posts into either a deleted mail folder or trash (Not sure why I have both) These are posts from groups I belong to where I receive most of the mail in my inbox. I have also had personal emails from family that were important but I only discovered them because if there is a dot by the trash showing unread mail I have to check it. I thought somehow it could have been my "rules" so I deleted all but a few of them and the problem still occurs. I would like to reset my mail configurations as there seems to be unnecessary folders. I am just not sure what to delete or keep when I do this. Also, I have certain posts with information that I want to keep so if I reconfigure it I want to be sure not to lose those.

On iCloud I have the following mail boxes set up:

icloud (4 accounts)

Hawaii.rr.com

GMail (3 accounts used primarily for junk)