One thing you might want to try is having your trapped kerbal get out of the cockpit at apoapsis and then push against the front of his spaceship using his EVA suit. Since you're already so close to entering the atmosphere, you'll probably be able to slow his ship down enough to drop his periapsis into the atmosphere. This way you won't even need to have a second ship rendezvous. Be sure to point the ship prograde before getting out and pushing. Also, make sure to get back in after pushing to check if the periapsis has dropped enough. Then, just sit back and let the atmosphere do all the work. If you do want to attempt the rendezvous, make the second ship's apoapsis higher by a decent amount by burning prograde at it's periapsis and then wait/timewarp until your closest approach becomes very small. Make sure you set the first ship as your target, and when you reach your closest approach time burn so that your relative velocity to the first ship is zero. Then it's a matter of burning towards the first ship so you approach it and then burning again to make your relative velocity zero when you get close. It may take a few tries to really get the hang of it. That's why I mentioned the first method of getting out and pushing. Rendezvous are made a whole lot easier with RCS.