It is really hard to offer any help when you don’t specify what aircraft you are flying. Quite frankly, I’m not sure there is even a problem for YOU to sort out. It very well might be the sim and the aircraft and/or the incomplete modelling of systems.
Terminology you use in your post leads me to believe you are in an airliner, and in that case I lean heavily towards it being a MSFS2020 issue.
But, assuming it isn’t MSFS2020… here is how it “should” work.
TL;DR make sure you have your MCP altitude set to the glideslope intercept point alt – and that you are below that alt when you want to intercept and follow GS. Make sure you have the ILS freq dialed into both NAV radios, and the CRS knob(s) set to the ILS course.
You program an arrival in your FMC and fly it with autopilot, both LNAV and VNAV and adjusting your MCP alt along that arrival. Along that route you get assigned a runway via a transition, and you get cleared to that transition IAF and cleared for that approach.
Now it is time to put that approach into the FMC, and activate it.Time to put that ILS freq in the nav radios, set the CRs knobs to the runaway course, and set your MCP ALT to what that IAF says your alt should be at that point.
I actually usually set MCP ALT a little lower, at the altitude the approach says will be the GS intercept. Note, that won’t make autopilot put you at that altitude when you arrive at the IAF – it just tells the autopilot that it is allowed to guide the plane further down past that IAF.
As you near the IAF, your FMC will probably indicate it is time to DECCELerate. Since you have autothrottle (AT) on, it will try to do this, but you may need to help with speedbrake, and extend flaps a few notches when at the right speed.
As your AP continues to follow the approach, at some point you will be on a path to intercept the final course, and your aircraft will probably be below the glideslope (GS). If you are flying in AP HDG mode, then you can’t yet set HDG to runway course. But if you are in VNAV mode, go ahed and set HDG to runway ILS published course.
This is where you want to be. in order to intercept LOC and GS. Below GS is important. As you get near the intercept point(s) you will see LOC diamonds become solid, and the GS diamonds become solid. Now it is time to hit the APP mode.
Once the APP mode is active, the aircraft should intercept and follow the LOC and also the GS and then descend on the GS. You shouldn’t have to do anything.
That said, if you have forgotten to put the CRS knobs to the ILS course, and/or the HDG to ILS course, then things aren’t going to work as expected.
But if you did everything right, the aircraft will intercept and follow LOC and GS, and now it is time to get flaps and gear in landing config and the speed set to Vref + 5kts. Unless the aircraft is equipped and certified for autoland, you should disengage autopilot and autothottle around decision height, or at your discretion.
Now, I can do as described above all day long and not have issues in any other sim (even in default aircraft) But I haven’t had a lot of success getting the 747 or a320 in MSFS2020 to really work as expected. But to be fair, I haven’t spent too much time on it because I am convinced it just isn’t really ready. Autopilot is too buggy and avionics modelling not mature and incomplete.
The majority of my personal experience is in Boeing airliners and avionics in other sims.