I recently tried this kit out. As mentioned by the manual, it does clean-up the remainder of nucleotides, primers, etc and at the same time somehow normalize your samples (within the range of 2-4ng/ul) which is great for saving time to avoid manual normalization (which could be very time consuming when you multiplex many samples). While Qubit or q-PCR assays can accurately measure this final concentration for the pooled library, to me it is not very comfortable to deal with such a low concentration at this step (you will need to dilute the pooled library for several other steps to reach to the final concentration required for sequencing ~ 5-20 pM). I personally prefer to measure my PCR products by PicoGreen, do the normalization manually, pool the samples, and cleanup the final library with a column clean-up kit.  

Using a fragment of the plate is also doable; just carefully cover the rest of the plate for future use. However, I don't see why you should be concerned about discarding the plate?  As far as I know, the plate is not special and you should be able to use any 96-well PCR plate with the remainder of the reagents.  

No, the plate is coated with a binding agent. Don't throw it out.