Can you identify what couplers your cars and locomotives came with? We might be able to give better advice if we know.
To delve further in depth to what others have said, truck mounted couplers, regardless of what coupler is installed isn't the greatest idea the manufacturer that came up with them had. If your train is only ever pulled along the track they can work ok, but not great. Start pushing your train and you will come in to heaps of frustration as the trucks are forced out of true alignment with the rails with the usual resulting derailments. Deep flanges are required to keep wagons on the rails.
Body mounted couplers are the best way as that force that forces the trucks out of alignment can't happen, and no surprise that's how it is out in the real world. Ok, there were examples of truck mounted couplers in the real world too but they were all locomotives as far as I know.
As to choice of couplers, If your models have horn-hooks, my advice would be to replace them with anything in the below and smash them with a hammer.
Kadee makes quite a range of couplers, including some that are supposedly (I've never tried them) direct replacements for replacing truck mounted horn hooks. They are available just about everywhere and most train shops would probably be able to advise on which ones you could use. Kadee also has a conversion chart on their website that lists models and what couplers can be used in them
Like a few others here I use Sergent couplers. These are the best in prototype faithfulness and I fully support the short way Jacob mentioned them; there really is no comparison and that's the way I would promote them too but I also realise they are not for everyone. They must be assembled and painted just like any other kit and if that's not your "thing" or your dexterity isn't the best then you have to decide if you want to or can do.
- Tim