Alright, I have used BaseSync MFD and I think I am sorta close to doing the right thing. Here's my strategy so far:
1) Use BaseSync to watch for how many orbits until closest approach where it says "Time: Dist: Heading:".
2) When it reads 3 or 4 orbits away, make a normal or antinormal burn when you cross the earth's equatorial plane (indicated by the gray line in BaseSync as well as the "Tn" reaching zero as long as you are in equator mode and not direct mode).
3) Watch the highlighed "Dist:" line and keep burning until the distance goes close to zero. Now your orbit passes nearly directly over the base.
4) Press the "DEO" button to get to deorbit mode. (The following is my guessing) Then set your entry angle to about 1 degree, "anticipation" angle to 3 degrees (I'm not sure what this affects, but this angle is explained in the manual that comes with the MFD), and set the reference altitude (RA1) to 40km (I believe this is just where you expect the most deceleration).
5) The MFD should now show you where and how long to make the deorbit burn via a white line and the "BT" burn time. Do it. NOTE: a recent revelation to me was that the shuttle's OMS engines are tilted 13 degrees up, so make sure you pitch up an additional 13 degrees from retrograde attitude before burning if you use the shuttle.
6) Turn normal or antinormal and burn again at the node in equator mode or direct mode (I used equator mode) until your the highlighted "Dist:" parameter gets close to zero. The reason you have to do this again is that by doing the deorbit burn, you slowed your craft down, so the earth will have more time to rotate underneath you, and that changes your impact point.
7) Use AeroBrake MFD and use "PG" and "PRJ" buttons to change your view to the map that shows your orbit. Rotate prograde and wings-level attitude, and pitch up until your AoA is about 30 or 40 degrees. You can use the MFD or the ship's autopilot to keep AoA and bank attitude.
8) From here, adjust your AoA and bank until AeroBrake shows you hitting the base. In its map view, there is a zoomed-in view of the target and your path in the upper-right corner.
9) After this, I am probably doing it wrong. The altitude vs. velocity page on AeroBrake shows a fairly smooth gray line going down to the surface. My actual trajectory is green and fairly bumpy which means I am doing a type of skip reentry. So, instead of spreading out my heating and deceleration over a longer period, I am doing a lot of deceleration right at the very end. I guess you would adjust your bank/AoA to get a smoother trajectory down to the surface.
So, this is NOT a tutorial, but a recount of what I have learned and done so far. I would love corrections and clarifications so that I know what I am doing wrong or improperly, especially about #9. Feel free to rip the correct parts off for a tutorial or whatever.