I would recommend staying in Marbella and visit Puerto Banús on as many occasions as you like. Puerto Banús is likely going to be very expensive to stay in, and so are the shops, restaurants or bars that you go in. You can see very good cars and yachts, and luxurious hotels. Puerto Banús is the place where the rich and famous stay. Thus, unless you are born with a silver spoon it is better to stay at Marbella than at Puerto Banús.
Some people might like staying at Puerto Banús because of the nightlife, the beaches, or just the fact that you might bump into some famous person. Or probably because they can afford it “so ¿why not?”. On my part, I have never stayed at Puerto Banús, I have gone for a walk along the promenade to see the lifestyle of the rich and look at the luxurious yachts and to enjoy the nightlife.
On the other hand, Marbella is much quieter. The historic center is really a charming little neighborhood. A place to dine there is "Plaza de los Naranjos", a square in the middle of the old town surrounded by orange trees with good restaurants and pleasant atmosphere. Staying at Marbella does not mean you cannot go out to Puerto Banus for its nightlife. You can go to one of the several discos and bars around the Plaza Antonio Banderas, like Funky Buddha or Seven.