It would be a good idea to sanitize with regular chlorine until you get your levels straight. You don't want your SWCG on while salt is still dissolving, as it will read high and potentially damage the cell. You also don't want to run it with the salt level extremely low, the controller would have to boost the current flow potentially reducing cell life. If you wait to sanitize you could end up with algae in your newly lined and filled pool.

Treat it with standard chems, once you've got the levels pretty stable then turn on the swcg to maintain.

If you add bleach while filling (probably a good idea). Make sure you don't get straight bleach directly on your new liner if it's not a white liner. You don't want to fade it out.