We recently completed the GGW in 4 days but I would suggest taking 5 or 6 to complete. Most walkers we met had their bags transported from one B&B to the next but we chose to carry ours. As we had just completed the West Highland Way we were staying in Fort William at the Bank Street Lodge in a double room. The staff there are very helpful and the self-catering kitchen is well equipped and very clean. Our first day was quite long as we walked to the Great Glen Hostel in South Laggan Locks. This hostel is very clean, has a very large well-equipped kitchen plus a spacious eating area. We had a private room which was a bit small but comfortable none-the-less. They also have a small shop to buy food items which comes in handy as there are no shops in the area. You could also make a shorter day by staying in Gairlochy. The GGW follows the canal for a long way then heads up onto the hillside. Unfortunately for us there was active logging in one part so we were forced to wait 45 minutes before be allowed through. This, plus the heat made for a really long day. The next day we walked to Invermoriston staying at Darroch View B&B. I'd highly recommend this B&B, very friendly hosts, lovely spacious room and a great breakfast. Once again I would have made this day shorter by staying in Fort Augustus then going to Invermoriston the next day. There are plenty of places in Fort Augustus to stay and lots of places to eat. If you make 2 days out of this section it will give you time to wander around each village. Invermoriston has some lovely easy short walks that we did not have the time to do. After leaving Invermoriston we walked to Drumnadrochit and stayed at the Loch Ness backpackers hostel. If doing it again I would not stay here, our double room did not have a lock on it and the hostel basically shared one bathroom (2 toilets and 2 showers). The self-catering kitchen was fine. From here we walked to Inverness, staying at the Bazpackers Hostel, conveniently located around the corner from the Castle. The host is very friendly and helpful. Our room was clean and reasonably sized.
Hope this info helps. We had a lovely walk along the GGW but didn't see Nessie