My son takes the same class (clonidine for him) and it did make him sleepy at first (wish it still would sometimes, sigh)...he is on both a long acting patch form and booster short acting pill doses during the day. His BiPolar (BP) has never been low on it. BUT he does have anxiety reactions where his heart pounds and I was just thinking of that for your son, not sure if he has any anxiety but to maybe be careful how much you monitor because if that was my son he would be scared he was dying or could die on the medication and that would then counteract any benefits we were getting.
It could be adjusting to it but of course it could be just too much for him and he may need half of the increase instead. There are other medications in the class and maybe this one is not the right one or as others have said maybe he would do better with the short acting form.
By keeping notes of when you give it and when he has these sleep episodes...you will be able to see when the blood levels spike and the dr can figure out if there is a better form, time to give it, or if does needs to be adjusted, etc.
Take deep breaths yourself, medications do need to be watched carefully but we of course have to do a lot of self talk to make sure we are not putting our worries on our kids too. (I have done that and then have to do a lot of back-pedaling, smile, so I am not criticizing, just responding to what I can relate to.)