The Union people were harrassed by the Confederate home guards in Winston and Marion Counties.However, this turned into a two-way street.A Union-minded man named George Stout formed an organization known as the Banditto Association that headquartered near Pikeville (in Marion County) and wreaked vengeance on Confederate sympathizers and their families.As retribution was piled on top of retribution, lawlessness finally reigned in NW Alabama during the latter stages of the war.This included roving thugs not connected to either side who were stealing things and, in some cases, raping women.
In partial answer to your last question about if the Union people came through that part of the country, how could they tell the difference between people who sided with them and those who were Confederate-leaning?:When Union Gen. Wilson led his raid into the heartland of Alabama in 1865 (with thousands of mounted soldiers), he purposely went through Winston and Marion counties, as he figured he would have support there.But it didn't matter whose side someone was on, Wilson's soldiers took food, cows, horses, mules, etc. from them.In one instance a Union man in Allen's Factory (near present-day Bear Creek)had two bee hives stolen from him by these soldiers.I'd like to have seen that.
A few years after the war was over, the federal government set up the Southern Claims Commission, whereby people in the south could be reimbursed for things taken by soldiers.To be successful, however, claimants had to prove that these things had actually been taken (e.g. have witneses to verify) and that they had always been loyal to the Union.The testimony made before the this commission is available today from the national archives and is very fruitful ground for Civil War historians. I have used it extensively in my own research.