Are you referring to courses created through a SIS import? Regardless of how the course was created, student and teacher login would be the same using LDAP. Each section in cross-listed courses retain their SIS IDs, manually created courses don't have these, but it shouldn't matter in the grand scheme of things; though I'm not sure this is ok if you have some type of secure grade pass back to your SIS or student portal. We don't do this so I can't speak to that scenario.
You have a couple of questions here. The first is whether you can crosslist a manually created course with a course created by a SIS load. The answer is yes. As users are enrolled in sections, an ongoing SIS enrollment load would use the SIS ID for the SIS-created course's section. That should also not be an issue. The second question is whether your institution allows teachers to crosslist sections. We do not allow this, preferring to keep this capability at a more administrative level. That question depends on how your Canvas permissions are set up.
Not sure about grade pass-back. I think it might work, even though it would probably ignore the grades for users in the manually created course's section(s).
We are giving the Canvas Admins area a little bit of love (especially questions that are really, really old) and just want to check in with you. This will also bring this question new attention.
Were you able to find an answer to your question? I am going to go ahead and mark this question as answered because there hasn't been any more activity in a while so I assume that you have the information that you need. If you still have a question about this or if you have information that you would like to share with the community, by all means, please do come back and leave a comment. Also, if this question has been answered by one of the previous replies, please feel free to mark that answer as correct.