Hi there,
I am unsure exactly what you want to do, but it sounds like you have dreams of making a scenario. Which is Great!
The process you've been using however is wrong. When you want to make a scenario, there are basically two ways to begin.
a). Starting from scratch (or from a masterfile, rather), by using the button "Editor" on the first page you get when loading up ATG. This will start up a dialogue where it will ask for the dimensions of the scenario you want to make. It will then generate a map, where there is only one type of landscape on it, 1 hex that is of a regime that has the name default.. etc... Basically a barebones starting point. From there you then can either import (by setting a masterfile, which is basically another scenario)... This is a lot of work, all of it.
b). You can change a scenario that already exists. You do this by loading up the scenario, and then pressing the button called "Edit". It is down to the left on that screen. This will allow you to edit a scenario, with it's current masterfile, again this just means the various menu items filled out, so to speak.
Basically that is the first choice you need to make.
Once you've done that, assuming you want to make new graphics, you are going to need to make a folder in the subdirectory Graphics, where ATG is installed. This will make sure that nothing is overwritten of the graphics when an update is made to ATG, where graphics could have been improved for the scenario you are making. Rule number 1 is, don't overwrite anything that already exists, as it can be overwritten again. So it also goes without saying that you will need to save your scenario under a new name...
That should be step one.
Now let's say you want to redo a scenario. Like it sounds like you want to. In that case, it may pay off to look around in the scenario bank, on the VRDesigns.net site. Believe me there are a lot of scenarios there that seem related to USSR in one way or another.
You could also poke around in the many scenarios that the game comes with. I believe there is a scenario called "Russia 41 Gold" in the subdirectory "New WW2". With minimal changes to the settings TO&E (what you described) can be added to it, that is if you are satisfied with it as it looks.
Many many many things I'd like to impart... but how much is relevant is hard to know... Keep asking
