Log and capture all your shots. Make sure you know exactly what shots you have and where they are. Create separate folders for each scene if it helps you to organise. Being methodical at this stage will save loads of time when editing.
With all your clips captured onto your PC or Mac, put them together in the right order, but don't worry about exact timing. This allows you to get a feel for how the video is structured. Once you have this rough cut, you can refine it by trimming and adjusting your clips.
When joining two clips together taken from different angles, try to make the cut occur during an action. For example, if a person is walking along, swinging their arms, look carefully at where the arms are and cut so that they continue from the same position in the next shot. If you do this well, the cut will go completely unnoticed.
Don't be afraid of cutting the shots down in length. It is always surprising how short a shot can be and still be effective. There is nothing worse than unnecessarily long shots. If in doubt, cut it out!