After changing them (I recommend taking care not saving over the originals, and keep your own modified version in a separate folder with a slightly edited filename). You can then import the symbols into the map using Symbols -> Import PNGs.

After that, you can open the symbol manager, and find your imported symbols (they will be at the bottom). Select all the new symbols, and hit the save as catalog to save it as a new symbol catalog. Now, open the new symbol catalog as if it was a map (instead of into the symbol catalog window), go to the symbol manager again, but this time, select the symbols and hit properties. From here you can set up options like symbol groups and random selection from groups. Just save the file normally when done.

From now on, you can load this new symbol catalog into the symbol catalog window when working with a map and use it like any other catalog.

Here's Wyvern's Travelling places of Embra, now in the atlas.

I still have two sets remaining in my backlog from these before being done getting all the Embra maps into the atlas.

Wyvern's Hilly Places of Embra are now in the atlas:

You can just list out all the hotspots

LIST -> hit T (for entity type) -> check the Action: 2D Hotspot option -> Hit OK -> hit D (for do it)

The great thing here is that CC3+ remember the checked option in the entity type list between maps (in the same CC3+ instance) so the next time you hit T to go into that list, the 2D hotspot option will already be checked so you don't have to scroll through looking for it every time. (You still have to open that dialog every time though to add entity type as a criteria)

It shouldn't be hard to write an XP module that lists all the links in a map either, and combined with the MULTIFILESCRIPT command should allow all links in all maps to be listed.

Lovely map. Great use of the style to create a nice atmospheric location.