NCrunch places the markers as adornments embedded in the source code. This approach has several benefits, such as lower risk of alignment problems, simpler implementation and better clarity as the markers are closer to the lines of code they represent.
However, there are also drawbacks. Code that does not make use of indenting or is set to use word wrap can overlap with the markers (as you've described). There isn't really a way to fix this at the moment. A task exists in the backlog to introduce a configurable tray to hold the markers so that they don't overlap with the code. There is a chance that this may be introduced with a minor revision in NCrunch V1, although it looks more likely that it will be post-V1 (i.e. in the V2 release late next year). Sorry, I realise this doesn't solve your immediate problem.
Cheers,
Remco