Paint stroke create new layer every time you complete one stroke, you will not be able to do what you want have gaps in the stroke (you can ad masks to your completed stroke layer on in the places you want to have a gap). It is just the way it works. You can also use paths not paint stroke tool to draw your shape and then you can convert them to paint stroke by pressing enter key. Make sure you have only stroke enabled not the fill.
Now that i think about it. it is not important to have one continuous layer. I tried just making a protracted drawing without lifting the pen, after a minute there was a noticeable drag on the system. This is probably why it is not a supported feature.
What would seem to make sense, though, would be to be able to set a function so that each new layer being created automatically is placed after the last one in the timeline,
so that they are arranged in sequence one after another, without having to set an in and an out each time a new line is added.
I hope it is possible. it would be a great way to work in real time. so that one could open a video clip, and be drawing on the clip as it is playing. and they layers are being created in tandom with the video.
What i would really like to achieve is to make handwritten subtitles by simply watching the video play on the canvas and writting directly on the clip so that each new layer is being arranged in sequence in realtime. This would be such a great way to use the program and it seems like something that could be achieved simply. i hope it is!