Play with all the bits you want, when but it comes time to tidying away put everything in a themed box - eg, one for animals, another for cars, or, one for outdoors themed, another for work themed, whatever works for you and the toys you have. You can get plastic storage boxes very cheaply in pound shops or places like Wilkinsons - you can decide what's best for you, whether it's a lidded box or open/basket-like.
Alternatively you could use small drawers - such as the plastic organisers, like this - and have a drawer per theme.
Have all of your boxes/drawers out and put them away per theme, your DS may even enjoy sorting them with you. You could put a picture on each box/drawer to indicate the theme.
reading through this and I sound like an article from an old, women's magazine
There is also a further step you could take, if he has a lot of stuff, which is to put away things that he doesn't really play with in a separate area, and if he doesn't ask for them within the month then charity. Don't add to the toys regularly and instead keep it more streamlined. However that's a whole other ballgame and may be of no interest to you!
I also think that if something is being used regularly, particularly in a certain place, then it should be as conveniently stored as possible. So if, for example, your DS is almost always playing with his toys in the living room, then have a series of boxes/drawers with said toys in the living room. Easy to reach, easy to throw back in once done. We have a similar system here (less themes atm as DS is younger and doesn't have much in the way of 'types' of toys) and it's much easier, I just pick up everything at the end of the day and chuck it into the relevant box. Our boxes don't have lids, because that would just be an extra faff for me 