There are 3 Rebel "armies" (Jackson, Ewell, Johnson), and their composition is diced for each time they are brought to battle. Each one is about the same size as a Union Division ("army").
The tactical rules are abstract, and instead of actually measuring distance, the battlefield is conceptualised as having Key Features, a reserve area, and a transit area where forces pass through as they move from one Feature to another.
Units/brigades tigger combat as they move into KFs. I suppose it's a bit like the Dixie card game, but with more granularity.
You can perhaps use F&F or BP for your combats, but this means spending a lot more time for the campaign.
Now I think if you are planning to play this campaign "as is", you need a dedicated group of players who can afford several evenings/weekends to play it to a satisfactory conclusion. They should ideally have some knowledge of the period and get into the spirit of being a "political" rather than "career" army officer, and keep in mind the longterm aim of the game – this isn't a "strictly military" campaign!
If you don't think you can get a dedicated group, but are still keen to use the rules as a bais for your campaign, I think it will be a good resource to have.
If I am doing it, I will use the map, the army lists, and the Rebel movement rules from the original rules.
Divide the Union divisions amongst your players so each player or team will have roughly equal forces. Ignore the rules for Prestige.
Have the players manoeuvre their forces on the map to try to bring the rebels into battle; when one player/team does, the other player/team will play the rebel. Have rules for recovery of wounded/stragglers/routers.
Award Victory Points per your tactical rule.
Play for a pre-determined number of turns, then total up VPs to see which side/team is the winner.
To end, I strongly recommend the rules as a source of inspiration, even if you don't eventually use them "as is". You may even apply the concept to other periods and theatre (perhaps Roman hunting Hannibal?).