A specific question on Rappan Athuk - I had a hard time figuring out all the interconnections between the levels. There is a map in the tome - but it wasn't great for my brain. To the OP - did you have any suggestions or tips on how to keep all the connections between the levels straight?
Yeah, the level-connector map looks like a circuit board schematic.
I put the image into RealmWorks (initially) and then Foundry. That allows me to link to maps. Mostly, I never need to reference it. For all my maps in Foundry I have it set up that when there is place that leads to another area in the dungeon I have a tile that links to a tile on the linked-to map. I just click and the PC token(s) are automatically move the correct location on the other map. I find this much easier than flipping to the other map and finding the correct entry point. Even with the map book, the page flipping can be annoying, especially for areas like the Bloodways that have a LOT of movement among multiple maps.
Also, one complaint I have about the Rappan Athuk book, and many of FGG's books in general (don't get me started about Tegel Manor), the editing isn't great. There are too many mistakes or unclear references in the maps or discrepancies between the maps and the text. Not a terrible amount of mistakes for a book this size, but enough to be confusing and annoying. FGG puts so much thought into the quality of the physical books. They are durable and expense. So it is disappointing to see some of the mistakes caused by lack of solid editing. I think they prioritize hitting their Kickstarter deadlines too much and don't take the time to properly edit. Kobold Press does a much better job with editing in my opinion.
Anyway, back on point. Prepping the maps in a VTT makes a huge difference but is a big investment in time. Now that RA is available in Fantasy Grounds, I would highly recommend it. If you already have FG, it is a no brainer to spend the $50 for RA. Even if you don't have FG, I think it is worth it to buy the software and prepped RA material given how much play time you are going to get out of it and the convenience and prepped time saved. Just having all the custom monsters and magic items stated up in the VTT would be a game changer.
With a VTT, and really, even when running from the book/PDF, I don't think the level-connector is going to be referenced that often. About the only time I reference it is when the party is doing intel. Questioning/interrogating NPCs, using divination, etc. to find a path to an area or information about nearby areas. Then the level connector map helps. It isn't the most intuitive map, but I'm not sure how else they would do it.