I think your right. Whenever I am traveling in Virginia on some back road, my father will point out Mosby Road, which gets its name from Mosby's Raiders. They were a group who operated out of a swamp and raided Union supply lines, and they were just one group of many. The war worked out perfectly to dissuad a larger scale guerilla movement, by having major CSA victories draw out larger Confederate armies, just to have them crushed at the end of the war. There are numerous situations in the war where the Confederates could have retreated into the mountains after a defeat and waged a long term guerilla war.
Well, I'm not so sure the psychology of the Confederates would have allowed for such. They had a 'Southern' identity, but both sides moral were very much tide to reports of victory or failure from the battlefield during the civil war. American newspapers, north or south, were pretty hysterical in that era. (And the people seemed to be too.) I'm thinking that by the time the South committed itself to resists principally through gurrilla warfare, it'd be only after its conventional armies had been completely defeated.
Also, adopting such a strategy so early on really cripples it in the eyes of foreignors, on whom it'd rely alot on for much of its support. I'm not so sure as many guns and ammunition get into the south, without the early sense of optimism / inevitability of the South's victory in European courts.
And even if the Union wins at 1st Bull Run, it's not likely to be able to move on Richmond before another army can be put in its way, assuming the Confederates put up half a fight.
Also, adopting a gurilla strategy would probably open up unionist areas of the south to invading northern armies sooner than otl, further undercutting their effort. (The appalachians, from Virgina, Tennessee, and North Carolina. Obviously, the south needs to use conventional forces there, as their gurrillas aren't going to be able to operate there.)
Not to mention the gurilla warfare becomes more complicated when an if abolition becomes a Union war-aim, although that's still not likely to happen until after the first 85,000k Union KIAs or so.
Attacking union lines of communication, and picking of security details, are all good ideas. But to be successful, there's still going to need to be able to keep the Union out of its major cities, drive it from the major rivers or hold the river forts, defend its own railroads and lines of communication, and ideally (though its hard to see how) keep open a port. All of which is going to take conventional armies.