There are a few different ways to fish clipped in. At a new venue or when you are looking for the fish, cast out your rod to a certain distance on feeling. If the rod runs, let it run until it stops and then clip in your line. You can now continue fighting the fish and when you cast again you are on the same spot where you got your run.
Another method is to walk out a measured distance and clip in and then reel up and cast. I do this when I want to fish at a predetermined distance like 90m.
These two methods only work for small fish because the lines remain clipped in. If you pick up a bigger fish it is going to snap you off. What I do when fishing a venue with big fish is to place 2 markers on the shore that are say 90m apart. Before every cast you walk out the 90m, clip in, reel up, cast out, unclip and put your rod down. You repeat this every time you cast. It is hard work yes, but I found that because you are catching bigger fish your run tempo is slower so walking the distance is not so much effort.
Yes, the sudden stop can snap your line and believe me it has happened a few times to me. You sometimes forget that you are clipped in at say 60m and you cast for 100m and SNAP! To stop this from happening you keep your rod pointing backward while the line is traveling, as it hits the clip you swiftly lower the rod to feather the impact and pull the tip below the surface. This pulls the line tight and cuts through the surface tension of water. A very effective technique when the wind is blowing. As you develope a feel for how hard the cast is to reach the clipped distance you can keep the rod upright instead of backward because you don't need to break the cast as hard anymore. Needless to say this technique doesn't work if you cast for 100m and you are clipped at 60m. You wan't to achieve a gentle touch down into the water.
I don't like tape on my line at all because it interferes with the line going through the eyes. Permanent marker on hi viz line does also work but it is not as accurate as clipping in. It is not always neccessary to clip in, especially in summer. Permanent Marker on hi viz line that you made a long black stripe on is good enough. You only need to be in the general area usually.