By 'tubes', do you just mean protrusions from both? Coz the male 'tube' isn't exactly a 'tube' like the female's, more of just a pokey thingy. Anyways.
How long has they been going at it? If you want to breed them - then I suggest leaving them in. Males always tend to be aggressive towards females, it's a natural thing. However you should always keep an eye on them, in case it gets really bad. As long as both are ready, they'll eventually get along and spawn and stuff. But if one is not ready (the jag in this case), then she could be beaten to death. But yeah if it's not extremely bad, then you can leave them be and hopefully they'll breed.
Also when/if they do breed, it may take a few tries for them to get it right - sometimes the eggs will be unfertilized, sometimes they'll get eaten, but chances are eventually it'll work.