You can add user waypoints on the REF NAV DATA page using Lat/Long, reference from an existing waypoint in the NDB (Nav Database) or any temporary waypoint you may have created such as an along track waypoint. These waypoints are stored in the temporary database and are deleted after the aircraft lands and the FMC recycles back into departure mode. These waypoint names can be anything from 1 to 5 letters or numbers and do not have to comply with the standard 5 character naming convention.
These waypoints can be inserted into the active flight plan (not particularly recommended but can be done unless forbidden by your company SOPs) or inserted on one of the fix pages as a reference, this is how we do it for ETOPS, as flight plan modification on the oceanic portion is forbidden at my company.
They cannot and do not interfere with anything stored in the NDB. The NDB cannot be user modified without the use of a data uploader. We as pilots cannot corrupt the NDB by entering anything.