Reapplying spar varnish/urethane to exterior door
The streaks should disappear with the first new coat of urethane assuming you haven't sanded into the stain or surface of the wood. The wood is probably stained or has darkened due to sun exposure, and if you sanded into the wood it will need to be restained or given time to darken.

As far as recoat time, follow the instructions on the can. Typically you can recoat as soon as the first coat has lost its tackiness, but read the label to be safe.