He leaves small spots in the whole house.. how do I train him for this.?

A little more information would be helpful.
For example: Is he still intact or has he been neutered?
Are there now or have there been other pets in the house?
It sounds as if he may be marking his territory.
Neutering should help with that.
Also cleaning the places he has already urinated in with a good enzyme cleaner.
He is still pretty young and proper training can sometimes take long while.
Persistence will be very important.
Refer back to the sticky about Housetraining one of members has posted a lot of good info on the subject.