I feel you.  I am new to M3 as well, but our company has used them for years.  The bank reconciliations are the hardest thing so far.  From what I have seen I am not sure if this is normal or not, but some items post directly to the GL without hitting the cash management.  Some of my hotels the Cash or the CLC deposits hit the GL but not the Cash register so you have to go in manually and check to see if they cleared by printing and highlighting them and then doing a "one sided entry" into the cash register for the uncleared items to clear next time.   I am actually here to see if I can find the how to on the "one sided entry"  I can't find my notes. 

    Also if you use the Adjust feature you can make quick JE, but you can't attach an image to that.

    Good luck!