There are thousands of different species of reptiles and they have evolved many different ways of mating. There is lots of complicated and interesting stuff that goes into the reproductive cycle but I gather you are asking about the act of copulation itself. I will try to briefly break down the major groups.
All reptiles (like birds) have a single opening called the cloaca through which urine, feces, and the reproductive tract passes. In snakes the males have 2 penises (called hemipenes) that are stored inverted inside the tail. When erect one of the hemipenes flips itself inside out and protrudes through the cloaca. The male snake will pursue the female by riding on top of her and trying to align their tails. If she is receptive to mating she will lift her tail and open her cloaca allowing penetration. Sperm flows in a groove on the outside of the hemipene. Most lizards have a very similar system. In turtles and tortoises the males have a single penis called a phallus. which is also stored in the base of the cloaca, and when erect it protrudes so it can be used for penetration. Males have curved bottom shells and long claws on the front feet that help them mount the female from behind.
The difference between a penis and a phallus or hemipene is that a penis has an internal tube (the urethra) through which both urine and semen pass. In reptiles the male reproductive organ has no urinary function, and semen is transported through a groove on the outside of the organ.
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