Clearing in is very easy, but the easiest spots are at Soper's Hole West End, Tortola or at Jost Van Dyke. Both of those harbors have mooring balls you can pick up for several hours without charge, so it is easy to go in, clear, and then move on. At West End, there is a wonderful grocery store called the Harbour Market which is at Soper's Hole Marina. The Customs Office is across the harbor at the ferry dock. For us, it cost $19 to check in and we think that allows you up to 30 days. To check out we had to pay $0.75. (yes, that says 75 cents). If you stay less than 4 days you can check in and out at one time, but there is far too much to see and do in 4 days.
If you want to anchor rather than take a mooring, it is possible. The locals think it is too deep to anchor most places, but they consider anything over 20 feet as too deep. The places we actually anchored are as follows: (1) Benures Bay on Norman Island. The wind swirls around so we and most of the other boats anchored in good holding sand and then stern tied to a tree. About in the middle of the curve of the Bay there is a trail leading to an overgrown road. It is about a 40 minute walk with great views over the hill and down into The Bight, which is a famous anchorage full of moorings. There is a beach bar with wifi. The room left for anchoring in the bight is right at the front of the mooring field to the right of the bar (looking from your boat as you come in). There is room for 4 or 5 boats to anchor, but be ready for noise. (2) Marina Cay, to the northeast of Tortola. This is a beautiful place with a restaurant on a little island. There are lots of moorings but we anchored just at the back of the mooring field in about 30 feet of water. Excellent holding in overnight winds of 20-25. At those winds, there was some swell coming over the reef. (3) Vixen Point, Prickly Pear Island, Virgin Gorda. This was the prettiest of all. There is a small mooring field off of the SandBox restaurant and beach, but just to the north of the moorings is lots of room to anchor in 15-25 feet on good holding sand. Here we had gusts up to 38 knots with no problems and flat seas. The view in the evening across the sound, with the sky streaked with color and late boats sailing into the harbor, was magical. (4) Inside Road Town harbor, right past the cruise ships and through the entrance leading to Village Cay Marina and the Moorings Marina, there is an anchoring area which can hold at least 6-8 yachts. The bottom is thick, gooey, stinky mud so a chain wash down is nice. It is totally flat and calm in there, and we used our dinghy to get to the best chandlery in the BVI, the Golden Hind, and then an short walk to a wonderful grocery store, called RiteWay. Go to the big one past Wickham's Cay II. By taking the dinghy to Village Cay Marina it is an easy walk to the ferry dock to clear in or out.
Other places we saw or have been told are good to anchor if you don't want to take a mooring: (1) Drakes's Anchorage at Virgin Gorda. We had a good view of the boats there while we were at Vixen Point, and it looked very good. (2) Deadman's Bay on Peter Island. Look for a sandy spot in the eel grass. There is supposed to be good hiking ashore. (3) on Jost Van Dyke, right up at the east end, there are some small cays and reefs. Go with good light and it is supposed to be easy to find a nice spot.