Having pre-determined groups of NPC tokens all brought in at the same time.

Im doing a game with fairly large open city areas. I've made custom map images to reduce the amount of tokens on the board and what not. However I was wondering if there is a way to lay out NPC tokens onto the map and then have them only be loaded in when the players have uncovered that part of the map. (Fog of War) Either that or be able to group the NPCs together where it will sort of save their distance between each other so that i can just drag and drop the entire group and just place it where it needs to be. If either of these are at all possible it'd be a great help. 

I take it you don't want to have them on the table but in the GM layer? You could lay them out on the map, then copy/paste them to a new blank map. Then when you are ready for them, just copy/paste them back from the storage map.

I do want them on the table so the players can see them when they uncover them. I just want to be able to either hide them from my view or like you said use a storage map, which I hadn't thought of and will definitely use. I'm trying to get the best out of performance because of the rather large area I figure with that many tokens on the map will slow things down. 

So I take it you don't want to use normal fog of war to hide the area they're in, with them already installed... You could use a storage map or for extra speed, I will sometimes have a fogged-out border or lower area on the map and have tokens parked there for later use. Then I can copy-paste quickly or just drag them to where I need. (I could grab them from the GM layer but I think that's faster, for me.)

Fog of war bro.  Put them all down, turn fog of war on, and only reveal it to them as their characters can see the area/NPCs.

I use the GM layer for my hidden tokens, you can then either utilise the  Bump script (since you are a Pro subscriber) to reveal them quickly from the objects layer or master the use of the  layer based keyboard shortcuts (which is what I use) to quickly switch to, move tokens from, and switch back from the GM layer :)

My recommendation would be to separate the city into different sections. You can even drag individual players to different sections of the map. They will only load the section they are on. Its how they made the Elder Scrolls Oblivion's capital city so amazing without overwhelming players.