Woohoo! Just followed Jarvita's advice! It works awesome! :woohoo:
Here's my guide to what to do (well, it worked once anyway... :shifty

:
1) When in an orbit of 300-400 km, get in the same plane as your base.
BaseSync MFD (right at the bottom) is perfect for this, showing you how close your orbit comes to the base. You need to follow the instructions really. If you're not bothered about fuel/numbers, just do it by eye using MapMFD zoomed in as much as possible.
2) On the orbit that goes over the base, make your reentry burn when you are exactly(ish) on the opposite side of the planet to the base. Sounds naff, but works for spaceplanes well. You can tell this using BaseSync MFD or MapMFD. Use OrbitMFD, and stop burning when your... errr... lowest bit of your orbit is about 40km up. (I can never remember the names...)
3) You're now coming in. Don't use MapMFD to judge where you're going to land! It ignores the atmosphere and so gives wildly wrong readings for the land site (small square at the end of the orbit lines). Use the marvellous [ame="http://www.orbithangar.com/searchid.php?ID=2139"]AerobrakeMFD[/ame]. It does loads of complicated reentry stuff, we just want the map bit. By pushing various combos of the MOD and PG buttons, find something that looks like MapMFD with a little map inset. This is it! It shows your glideslope, taking into account the atmosphere.
4) Point your ship forward. Use whatever Attitude autopilot you have and point your ship with a AOA of about 45 degrees. Make sure things like nosecones are shut... :lol: By about 100 km up, put yourself in "reentry" thinking mode. We're going in.
5) As you reenter, keep an eye on AerobrakeMFD. Watch how your orbit land site suddenly shoots shorter and shorter. The inset map shows a zoomed in view of the base; use it to keep the end of the orbit/glideslope on the base. Each square is about 100 km across. Pitch up and down/ left and right to fine tune your glideslope in.
As a rule of thumb, a vertical speed of above 100m/s in dangerous - you'll heat up too quick to recover and.. well... let's say your base will have a nice impromptu shooting star display...
6) By 20 km up, you should be close enough and slow enough to switch to aeroplane mode, exit your autopilots and land your ship.
Phew.