Hi Gabe,
you can do it like that. As amaroli is happening here aswell in the morning, if semen goes into the urine it will go back into the body aswell. But if you loose some semen here and then it is no problem at all. If you are into practices even if you lose some more semen, it will not be a problem.
Btw, even if the nervous system is purified it can still happen. E.g. in phases where you are in relationship with a girl it can happen again even though it did not for months or even longer. Sometimes if you have practiced well for some months and reach some uber-state, the body may release some semen to ease off the energetic pressure.
You are lucky if you wake up before it gets critical, here it is a mixed thing, But I do not care much anymore. some years ago the effect of loosing them was greater, now it makes a difference of about 10% perhaps
Do you practice some kind of meditation and pranayama daily?
Peace friend