Reliant and Enterprise both went to Regula One, but Reliant was first. By the time Kirk was trying to contact Dr. Marcus, Khan was already close enough to jam their transmissions. The lead scientists beamed down to the Genesis cave, Khan discovered the remaining scientists didn't have Genesis handy, kill nearly everyone, then runs off to confront Enterprise.
(Side note: Did Khan actually dock Reliant to Regula One or use a shuttle? He must have, because none of his crew bothered to check the transporter room. And why didn't Dr. Marcus delete the logs? Very lucky for Kirk, but unlucky if Khan had known about transporters. But Khan HAD to know about transporters, because he read the entire technical manual for the original Enterprise, and used that knowledge to beam his revived crew back in Space Seed. This is just sloppy work on Khan's part!)
In the first encounter, Enterprise loses its Warp Core and Impulse drive, and is on battery power. Reliant loses photon torpedoes and its Warp Core (and therefore phasers). At the end of the first action, both ships are crippled, but only Enterprise appears to have any offensive capabilities. (They've nearly drained the emergency batteries, but Khan doesn't know that). Khan withdraws from weapons range, and both sides scramble to repair systems.
Impulse power is restored, giving the Enterprise enough engine power to make it to Regula One. Remember, though, that Reliant still had Impulse, while Enterprise had to repair it. Therefore, Reliant was able to make it to Regula One, and hide. Khan knows which vector Enterprise will be approaching from (based on their confrontation location and Regula One), so Khan moves his ship opposite of Regula One to put the bulk of the planet between himself and where Kirk will pop out.
Khan knows that Kirk will also be looking for Genesis, and that he's more likely to be able to find it than Khan would be. Kirk knows this too (so clearly, I cannot pick the goblet in front of you! Sorry...), and he also believes Reliant's warp drive is still offline so he and Spock talk in code; "by the book, hours will seem like days" and the transporter needs two days to be repaired.
Reliant is still listening in, so when Kirk and Co. locate Genesis, Khan beams Genesis up to his ship and abandons Kirk. He heard Kirk's order to evacuate in a day, and knows that the transporters will take two days to repair, so he's got time, and remember, Reliant's phasers and photon torpedoes are still out of commission, but are being repaired. He figures he has enough time to repair weapons, max out the throttles to catch up with Enterprise, and blow it out of the sky.
At this time, Reliant and Enterprise are both orbiting the planetoid, but on opposite sides. I don't remember if this was some of that "2 dimensional thinking" or if they surmised it because they couldn't locate Reliant anywhere else. Reliant couldn't destroy the Enterprise, but nor could the Enterprise destroy Reliant. Both ship's warp cores are down.
They're at a stalemate, and an unbalanced one at that; whoever repairs warp first wins, so Kirk finds a solution in the no-win scenario: the Mutara Nebula, which is conveniently located at Impulse Drive distance (a lot of conveniently located in this movie in order to have the "warp drive is broken" plot element, but I digress).
At this point, Kirk puts the pedal to the metal to the nebula, and Reliant follows. One thing many people forget is that, unlike "Warp Factors," there is no definition of distance-traveled-over-time for Impulse drive. Impulse is ordered like a naval ship would ask for power; in fractions of "Full Steam". So both Reliant and Enterprise are running at Full Impulse, but Reliant's full impulse is just a smidgeon faster. As such, Reliant finally gets into weapons range just in time for Enterprise to enter the nebula. Note that the nebula interferes with sensors on ships inside the nebula, so Enterprise is blind but Reliant isn't yet!
Kirk goads Khan into entering the nebula as well, so we can have a submarine movie in space, and the movements become really complex. Kirk outsmarts Khan again, Khan spits at thee, Spock dies repairing the warp drive, and everyone lives happily ever after. Except for Spock. Because he's totally dead.
