Young puppies can’t hold their bowels & bladders for long. If you come home to find that they’ve had an accident in there it’s quite possible that they can’t hold it that long. Generally puppies can hold their bladder for about one hour per month of age. So your 3 month old pup can probably only hold their bladder for about 3 hours. If you’re going to be away at work for long periods of time see if you can get a neighbor, relative or dog sitter to come over to let your pup out during the day.
I don't teach or recommend so-called "purely positive" methods that allow misbehaving pups to continue misbehaving, instead of teaching them which behaviors are and are not allowed. "Purely positive" is fine for teaching tricks and high-level competition exercises, but NOT for teaching the solid good behaviors that all family dogs need to know, and NOT for stopping behavior problems such as barking, jumping, chewing, nipping, chasing, etc.
The process is the exactly same for older dogs as it is for puppies; prevent accidents from happening by using baby gates and a crate if possible, create a predictable schedule, learn to recognize your dog’s potty signals, accompany your dog outside and immediately reward for all outdoor elimination, properly clean any accidents and supervise your dog until you’re sure that he understands the rules.