Tim. I have done that, so it should not be a problem. I assume you have a sketch in each part and they are visible in the assembly and you select both and then mate? Should work. I sometimes do this with centers of rotation before I have the features necessary to create "real world" mates.
A better practice, and maybe a time saver, is to use planes to mate. If you use the lines, you may need extra mates to define the xyz. Either use the world planes - which may already be where you want them depending on how you model - or create place where you want them. I think you will find that more controlled than with construction lines. But in the end, it really depends what you are doing.
Daniel