I used to live just up the road from Fort Augustus years ago, things may have changed a bit, but there's some really good flowy natural single track trails around and along the river at Auchterawe (on the edge of the village) and a could of good tracks at cherry Island about a mile up the glen towards Inverness.
Longer routes, go long the great glen cycle route to invermoriston, up the glen road towards sky then (quite a bit on the road about 10 miles-ish) then take the General wades road back over to fort Augustus, can be quite boggy, but nice wilderness feel.
Or go the other way long the cycle route towards Fort William, up the canal, at Invergarry follow the mandally road all the way along instead of taking the cycle route turning, there is some nice single track trails at the forestry commission wood at the end of the road and then you can take the single track back along the north side of the river back to near the hotel in invergarry, were you can re join the cycle route. This bit is going back on the same tracks as you came out on but is one of the best bits along the Great Glen cycle route, being mainly single track.
Hope that is of some help.