From the sound of things, I'd say you aren't doing the De-Orbit burn correctly, and are coming in too steep. First, consider when to perform the burn - and remember that too soon is much better than too late. The altitude of your current orbit affects this, the higher you are, the sooner you need to burn. From a low parking orbit of ~200k, burning 14.5M from the target is fine. Coming in from a higher orbit like the ISS's orbit you'll want to burn at least 16.5M from the target. 17M to 18M is better, but you can de-orbit up to a full orbit away and make it. Burning opposite the target is probably the easiest, as you get a nice gentle ReA (will be less than one degree), and a bit of a "rollercoaster" up and down glideslope.
Second, consider what PeA you desire. The later you de-orbit, the lower this needs to be. For a longer, gentler ride you'll want a PeA of about 50k if de-orbiting half way around the planet.
Keep in mind that AerobrakeMFD doesn't consider aerodynamics until you are under 200k, I usually start orienting the vessel for re-entry at 150k. Use the <MOD> and <PRJ> buttons to get the planet map display, and pick an AoA and bank that result in the green line showing your predicted trajectoy to end a bit short of the target. Anywhere within a couple hundred kilometers is fine at this point. The "Dist to base" shown is the distance between the end of the line and the center of the base.
If Aerobrake shows you on target with an AoA of less than 40 degrees, you can pretty much ride it out with small adjustments to keep the target aligned - remember that it's best to keep things a bit short at first. It's easy to extend the glide later, if you have to shorten it you'll get into heating problems.
The Home Direct tutorial mentioned above shows how I manage all that. From the point where I'm down to suborbital speeds and turn upright it's a pretty standard re-entry. You can watch the AoA indicated in SurfaceMFD to see the small changes in AoA. You'll also see how I offset the target so that I come in a bit to the south of Canaveral so I can make a 270 degree HAC turn onto my runway alignment.
Other than that, it's just a lot of practice. I've flown hundreds of re-entries to get to the point where I can usually nail a deadstick landing.