Your side glass needs no sealer, obviously.
WIth new rubber your guy will probably use dish soap or canola oil to coax
the fitted glass (no sealers in the channels) into their respective
pinch welds on the body. My experience is that these usually fit VERY tightly
when everything is new & will need no additional. If, after a water test,
it is determined that further sealing is required then it could be applied
carefully under the lips of the rubbers.
Others may have different experience.