I suspect that one or two folks have the lost the bit about this trip being in solid IMC.
I suspect not. If you're flying under IFR will your accuracy be less if visibility is lower? Either you can navigate, or you can't.
That said I've got two VOR/ILS a DME and a ADF and I'll have 'em all tuned idented and selected if they're available as well as a chart on my lap. I see no harm in having belt, braces and a piece of string to hold up one's trousers in IMC.
There's no question that you should avail yourself of all the resources you have handy. One shouldn't presume, however, that simply because instrument conditions exist, one can't navigate without a GPS. If one can't get by without the GPS, one perhaps ought not go in the first place.
We had to load every single point using lat long coordinates for the complete trip from Saudi Arabia (Yikes) but we double checked and confirmed each item and then checked againt the maps.
When I do a long trip (long being 7,000+ miles), the loaded flight plan can go on for twelve pages or more. I check every single waypoint by distance and bearing between waypoints, as well as verifying the latitude and longitude of every single waypoint, before departure. I generally enter it into at least three different GPS, INS, and FMS computers on board, and verify every single one of them. I also tune and identify courses, and keep track of waypoints one at a time during the entire length of the flight. Every few waypoints I verify accuracy of the nav, time over the waypoint, fuel, expected fuel burn against actual fuel burn, expected fuel remaining vs. actual fuel remaining, etc.
Verifying the data one is using should be a part of every single flight, whether the information is in a database, or not.
Use them all the time There are many reasons you may use a user created waypoint.
Absolutely. I do it all the time. Every oceanic crossing involves flight between waypoints, often marked by lat/long locations, and every one of these is manually entered before the crossing. As we reach each location, we verify nav accuracy shortly after crossing the fix and keep it plotted on charts as a record of what we did. We check our VHF nav against GPS and INS/IRS nav before going feet wet, and check it against the altimeters; it all gets recorded on charts to verify we did it and that it was accurate. Every waypoint is updated and the time over the next one forecast. We have to be accurate along the track and horizontally, and we must be within three minutes over every waypoint. It's absolutely crucial to keep verifying what's next, what's loaded the nav system in use, and current trends during the flight.
A flight which is slower due to headwinds will have a different fuel burn, will arrive over waypoints at later times, and may affect our ETA over this point or that point. Other traffic is being predicated on our ability to be where we say we are, or will be, when we say it.
These are no different than the techniques I used as a student pilot on my first solo cross country, and no different than I teach a student to use. Verifying the information, checking it regularly during the flight, and keeping it updated with current trends and changing conditions is elemental to the safe conduct of a cross country flight.