How do you choose a feature to line up on when approaching to land?
Probably the best thing to do is to start looking for your reference as you start to lose the runway under your nose. Hopefully at that point you'll be low enough to identify something that will stand out from the crowd all the way down to the ground. You may also favor choosing something closer in from the horizon at 2000AGL, to ensure you don't lose it behind the horizon as you descend. For me, flying out of Addison, it's pretty easy; the runway faces downtown Addison about 3 miles south-southeast (a row of corporate headquarters buildings along the Dallas North Tollway) which is far enough out to line up on but close enough and tall enough you'll see it right up until you pass the numbers. Flying into a more rural strip, you might have more trouble identifying a good reference that you can keep in sight as you descend.

Some potential issues with this general strategy:


Your reference point will lie well beyond the runway by design. Don't fixate on it; that will cause you to subconsciously stay higher than your intended glide path as you fly toward your reference, potentially overshooting the runway.
Your reference is a single point. That point and your aircraft make a line, which you want to be colinear with the runway. But, your aircraft is a moving point, so it's not necessarily true that you'll be in line with the runway even if your nose is on the reference point. Instead of one reference point, I'd pick two (even if they're not perfectly in line) and focus on keeping both reference points steady relative to each other.
If you can't see the runway, you may not be able to see surrounding visual aids like the glide slope indicators, which are just as important as staying lined up. Addison's PAPI lights are off to the right when approaching runway 15, which is stupid as my instructor can see them perfectly while I'm blind unless I nose down every few seconds to keep track (not an option without flaps).


While I wouldn't rely on it completely in VMC, if you have a VOR receiver aboard and the runway has an instrument approach, you can tune into the ILS frequency and use the "cross" alongside visual references to manage your approach during the time the runway is hidden from view. The ILS system is pretty well-standardized, while the visual references at each airport are not, so if you become accustomed to an ILS-augmented visual landing, the basic procedure can be applied to any airport.

The reasons I wouldn't rely totally on it include:


You're not instrument-rated (unless you are) so flying with your head in the gauges can easily kill you. Glance at it to ensure you're where you think you are, but rely on your visual references whenever you can.
You're not flying a pure instrument approach under IFR, so you still have to "see and avoid" even if you have tower staff spacing traffic around you (unless you ask for a "pop-up" instrument approach, effectively switching from VFR to IFR).
ILS availability/accuracy is not guaranteed in daytime VMC because the ILS critical areas are not required to be protected during these times. If you tell the tower what you're doing, they can advise ground traffic to use the ILS holds, but there may already be traffic in an ILS critical area and if so there's little the tower can do.
ILS may contradict visual indicators to varying degrees, because the ILS glideslope is projected from a different point along the runway than the PAPI/VASI array. You therefore shouldn't expect the ILS cross to be perfectly centered along the same path that gives you two white PAPI lights.
Radio-based ILS isn't available at every airstrip. In such cases you simply must fly a purely visual approach, and having relied on ILS to give you the proper glide slope instead of developing your sight picture will prove to be a crutch in such situations.