G'day, normally if ATC need you to track direct to a Waypoint, and it has no aid, then request radar vectors. Type in Lat/Long then track direct to the aformentioned position.
Hassles arise when flying over some routes that need a position report every 2 minutes or less (some Russian routes). The "DelcoRemy Carousel IV" has room for only 9 waypoints.
Some sectors have over 150 waypoints!
The F/E can put the long/lats into INS3, this can be then cross checked by the Pilot not flying against the ERC (has Lon/Lats). He chks TRK/DIST.
SIDS/STARS can be loaded, INS acuracy then becomes a bit a an issue, especially if not enough DME's etc. for updates. 3+3T.
CheersandBeers