It sounds like you are double charging on your orders through a combination of packaging costs and USPS costs.
First of all, there are no weight limits on package types in our system. If you set a weight for a Regular Envelope in our system you are setting the weight of the envelope to be included with the weight of the items for shipping calculations. The same is true for cost, if you assign a cost of 5.95 for a package that is added in addition to any calculations that you set later. That would result in a 14oz book plus a 15oz envelope that costs $5.95 -- and if you are also using a shipping rule (either USPS or an additional flat rate) you're getting another approximate $5.00 charge.
Fortunately it is easy to set flat rate shipping within our system. The most important thing to note is that you don't need to use every setting in our system, just the ones you want. You can skip package settings entirely and set a single flat rate $5.95 rule to apply to all of your orders across the board Alternately you can skip shipping rules and just set your envelope to cost $5.95 and that will be all that is applied to the order.
Also note that the number of items that can fit in a package is determined by the packaging capacity settings within each individual product, and that is a per item basis. There's no weight limits for what a package can hold, so if just one book can fit in one envelope you will want to set packaging capacity for the book to 1. That will basically charge the price of one envelope per book though, so you may want to consider increasing that number to the highest number of books you could ship in one package if you needed to even if it means using packaging that is not, in reality, a Regular Envelope.
If you can give us a -complete- run down of all of your shipping costs we can give you instructions on implementing them. Please give us the full information so that we can take all of your needs into account.