Try to concentrate your troops in a few arears, as is sure to expect attacks by mid-late 61:
Either
From Harpers Ferry / Manasas areas -> Towards Richmond
From Grafton -> Toward Richmond
From Norfolk / Butler Command-> Towards Richmond
From Kentucky -> Towards Nashville / Fort Donelson
From Cairo -> Towards Memphis / Corinth
From St Louis -> Towards Fayetteville
There are also those pesky raids -> defend with small garrisons / cavalry groups in the 2nd line, try to get them killed by supply
And finally sea/river invasions can go everywhere. Best defend good industrial areas with some units, but dont expect to avoid the invasion in the initial landing. Just be prepared to send troops by railroad from the nearst area.
Well sure there are a lot more of choices than these... but hope this can aid.