are you talking about PolylineOnMesh? you can simply deactivate vertex snapping it then will be as accurate as you draw it without being disturbed.
mesh boolean stuff indeed often makes trouble, my workaround is to convert the mesh with MeshToNURB to a polysurface and then use the regular boolean. that usually works. i must point out the success of this also entirely depends on the quality of the mesh, if it is not a solid closed mesh or has nonmanifold faces joining, that will cause hick ups so cleaning up your mesh is a must. sometimes if the mesh is dense it might need a few moments to think.
if that does not work post your file and somebody can try to get a working method.