However that got me thinking about something with these extra terrain slots in ToTPP that allow up to 16 different types that I haven't thought about before. Under the current circumstances do these extra terrains added into the game have their own special resources slots?
Yes, they certainly do.
These extra ToTPP terrains are added via terrain2 which supports extra rows added in whereas the 2 special resources slots for each terrain type is handled in terrain1 which I'm under the impression does not support new rows inserted? If that's the case then I'm guessing nothing appears in special resource slots on the map where extra terrains are used?
Not quite. Extra TOTPP terrains are added (in fact,
have to be added) with additional rows in Terrain1. I'm attaching the Terrain1.bmp from my Medieval Millennium mod which uses all 16 possible terrain types, to show how this is set up. This capability is enabled with the TOTPP "Extra terrain types" patch.
Separate from that, the "Terrain overlays" patch allows full customization of which terrain types utilize the Terrain2 file for overlay graphics. This means that any number (none, some, or all) of the
base or additional terrains can use the 16-image layout, and you have full control over which ones.
These two patches aren't linked -- you can use either one without the other, if you want.
If so then the fact that Mercator says his tool supports creating animations for these extra terrain special resource slots is interesting as I wonder how it works if the special resources are non-existent for those terrains. If there is no way to create special resource images in terrain1 for extra terrains but the special terrain positions are still there in the game (but just invisible) then maybe Mercators tool could be used to create a static (1 frame so no animation like Mercator suggests in the above image) special resource images for those extra terrains instead. So basically using an animation slot you'd be a creating the static special resource title graphic you can't currently stick in terrain1.
That's a clever idea, to be sure, but fortunately this approach isn't necessary since Terrain1 fully supports two resource slots for every defined terrain type. The only value in using CivSprite2 for terrain resources is if you want them to be animated.
I also feel like this system could also be manipulated to create multiple special resource types for the same terrain type.. eg 2 types of desert terrains that look the same in-game but when mixed together they allow for 4 different special resource types, all animating too should you choose. Such variety and extra decorations could definitely come in handy for my HoMM2 mod (there were so many HoMM map objects Metro & I ran of room to insert into Civ2) and Red Alert 2 (more burning city buildings!) so I'll have to do some more experiments at some point.
You certainly could create two "Desert" terrains that look identical but have different resources, giving the appearance in-game of a single terrain type with 4 resources instead of 2. But CivSprite2 wouldn't be necessary for this, unless (again) you want resources to be animated.
Remember, also, that the "Custom resources" patch allows
customized placement of all resources, i.e., they don't have to conform to any of the patterns available by changing a map's resource seed. This again works independently of the two patches mentioned above, so you can mix and match functionality however you wish.
"The Hinge Of Fate" designed by 
That's how the old, old Hungarian language mod from Apolyton was made.
