The PBS system allows you to correct the weight of the wrapped book when printing postage.  I'd just adjust it to cover the weight of the entire package.  But that's just me...

You definitely can use PBS for mutlibook shipments. If you have orders for all 3 the system should group them and print a bulk shipment label for you. If you are trying to mail a order that includes some freebies, then you will have to adjust your weight to include them all. If you have the option set to the weight of the book, then PBS will add a little for packaging, I think that is something like .6 oz. A scale is the best way to get the total weight, but you can find the weights on the books in Edit Book Data on the book details page or check Amazon for weights and add them up manually.

You do want to use something besides the wrapper to mail more than 1 book. You can select the 3rd label option and cut the bottom half of to include with the book and the top half use for a label. Box or wrap in tight heavy duty paper or use some type of bubble mailer (again tight to books). [Sorry if this part is obvious to you, but sometimes its not and the books are left exposed to the mean ol' USPS system].

I wrap the books and weigh them... then add a little bit of weight for the label.  You can print the label from PBS without using the paid postage feature and just print out a mailing label only.  As far as PBS shows, it will show that you have mailed out one book and you will get one credit.  The other two books are not tracked in any way... and make sure to remove them from your shelf when you add them as freebies. 

I sometimes wrap two average size mmpb together, but more than that requires a box or other shipping container.  There is a specific mailing label for that.