Two types of isomer are relative to MDMA and amphetamine/ meth.
R and S represent absolute configuration; where the order of placement of attached groups on a chiral carbon determines assignment.
D and L are optical isomers. Assignment is given depending upon how polarized light is deflected. i.e. is the deflection positive ((+) dextrorotatory) or negative ((-) levorotatory)
Optical isomers are NOT related to absolute configuration, but often an L will also happen to be an R (-), and a D an S (+).
Simply put, Isomers are different 3D representations of the same molecule. In these examples, D and L are like right and left feet (but with toes in odd positions that can't be superimposed on the opposite foot)
If The Shoe Fits...
It not a perfect analogy but in regards to receptor binding, think of it as being like a Right foot fitting a Right shoe.
The receptor that the drug is to bind with is a bit like the shoe, and the meth like the foot. Try putting a perfectly fitting left shoe on a right foot. It might fit with a struggle, but it's definitely not as easy a fit as the right shoe is.
Your receptors (and many enzymes and other bio-molecules) are also like the shoe. A molecule shaped correctly will fit in with ease, with the "toes" sitting nicely in their respective spaces. The opposite foot might go in, but toes are squashed up in places and loosely bound in others. It also usually takes some effort to squeeze on the boot (more energy)
Most biological processes including receptor docking, binding etc are energy efficient processes. If it don't fit properly in one place, then it might 'look' around for something else. In the case of L and D meth, D has a "best fit" with NE and DA target receptors. Enzymes pick up most of the non-bound L meth and metabolize it into hydroxyl (OH) substituted compounds which enable further metabolism or faster elimination.
D meth on the other hand spends quite a bit of time intimately associated with the receptors, chatting away and stimulating much gossip (secondary actions). Eventually the "janitor" enzymes come along and pick up the D meth, where its then carried through a similar process to that of the L. *
Some L meth will bind with receptors, although as mentioned it's hardly the snug fit D produces. However, the binding is an on again - off again relationship, so it's usually picked up by enzymes when "off again" D meth on the other hand may bind (on and off) for much longer, as the fit is more energy efficient. Sometimes the opposite isomer may bind as effectively, but causes little or no secondary actions.
Please note this is a very simple analogy. There are other things happening which don't necessarily apply to this model.
*Note: This a very simple and partly inaccurate model. Different isomers may be metabolized via completely different routes or via different intermediates.