As far as waypoints, on the route page where you insert the origin and destination, after doing that, hit the Next Page key on the FMC. There you can add jetways, individual waypoints, etc. Another way to add waypoints is on the legs page. As far as I know, you can only add custom waypoints on the legs page...not the route page.

Make sure you get rid of any discontinuities that may be there after editing your flightplan.

As for V speeds, I can't be bothered to do the work. If you click the key where you would normally insert the speed, RSK1 or whatever, it will automatically work out the speeds for you. Just do it for each one (V1, VR, V2).