krusbullen, most likely your problems mainly arise from two basic things - not starting the landing process early enough, and flying too fast.
First of all, there's the 'Rule of Three' - at any sort of normal descent rate, virtually all aircraft descend one mile for every three miles of forward progress. So if you're in an airliner at 33,000 feet, for instance, you should start your descent no less than 100 miles out.
Secondly, in most parts of the world, all aircraft are restricted to a maximum airspeed of 250 knots below 10,000 feet.
FS9 ATC is designed on the assumption that you are complying with those rules (and also following your filed IFR flightplan) and will therefore give you vectors and heights based on the assumption that you are starting off (from up to 30 miles out, when you first contact ATC for landing instructions) in the right place, and also low enough and slow enough to manouevre in plenty of time to intercept the glidepath and glideslope at the proper point. If, at fifteen miles out, you're off course, 5,000 feet too high, and still travelling at 400 knots, there's nothing ATC can do about it!
It's a good idea, as you start your letdown, to set the Indicated Airspeed to 240 knots. In the thinner air higher up, your true speed will obviously be much higher than this, but once you get down lower you'll be down to the proper speed. Use the default rate of descent or alternatively set it at say 2,500 feet per minute or so.
About the ILS not lining up immediately, remember that it's a flight simulator, not a railway one! The air is a fluid medium - the Sim will take it's time getting into line, but it will eventually get there! In any case, if there is any crosswind, the Sim will do the 'crabbing' for you, point the nose a few degrees upwind to keep you in line with the runway, so the Indicator may show you a touch off-line all the way down.
About offset ILS beams at some airports, as mentioned by rottydaddy, these are rare - but in any case you can forewarn yourself by calling up the Map, centring it on your destination airport, and enlarging the view. The approach path will be clearly shown as a green 'feather' and any offset will be clearly visible.
Finally, maybe see if this helps?
http://205.252.250.26/cgi-bin/yabb2/YaBB.pl?board=COF;action=display;num=1111322151