mhl78,
In reading about your situation, the first thing that I noticed is the error of having one clerk record the donations in MLS by himself. From the training, we learn: "The companionship principle requires two priesthood holders to be actively involved in opening the donation envelopes, counting the money, and recording the amounts [emphasis added] in the Church financial software. Having one person open envelopes and count money while the other person does something else is not adequate" (Processing Weekly Donations, slide 20).
Within the context of this posting, the error was not made by the two who opened and verified together. It was made by the one who recorded it into MLS by himself.
All of this aside, there also seems to be some discussion in the forum about having three people open together, count together, and record together. If I were asked my opinion, I'd recommend listening to your local leaders. They are more familiar with the details of the situation.
The general principles would dictate that exactly two do the work. I suggest this based upon the companionship principle balanced with a clerk's need-to-know. Obviously, just because a clerk has access to financial data, doesn't mean he should be exposed to them unnecessarily. However, as we all know, the Spirit (through the instrumentality of your local leaders) is the ultimate authority and can authorize any exceptions.