Places need to see your COMLEX to know you passed and know you can get licensed. You have to submit them mainly for that reason, but most places will likely ignore them unless they get a lot of DO applicants. Some places don't even know what the scores mean. Don't worry about that though. ACGME programs as a rule rely more and trust the USMLE more than the COMLEX, so it shouldn't really hurt you (obviously it would be better if they were both high though).
Just plan to take them both, and take practice tests a couple weeks out. If you feel like the USMLE isn't going well or its taking away from COMLEX prep then you can always cancel. That's my plan. Most people I know though haven't had this issue.