PIC007

Just to find out if possible (a) why are there so many waypoints on FSX maps that if you try to use them on your flight plan you get a message like, 'not in database', and your database has been updated?  Especialy the ones closest to airports.  Sometimes you run out of  waypoints
 
FSX database is 7 years old and never changes. The FMC uses more current data and reflects recent data, including name changes, runway ID, frequencies, etc. One way to simplify things is to file a flight plan VOR to VOR instead of "High or Low altitude'. The 5 letter designators are intersections and reporting points, useless in FS.  This is assuming you are creating your FP in FSX and not another planner.
 
 
  Also, having started to fly  IFR recently, the ATC will give you sometimes a  runway to land that is not the one you had on the flight plan? Does this mean that you have to quickly change your FMC legs to accommodate the new ILS  value, the approach waypoints and of course the runway number?  If you change it too late, you will have to go around and not be able to stick to your final approach plan or in a worst scenario loose it..
 
You should check the weather at your destination prior to departing to get the wind direction, as runway use is determined by that. You should also check the weather while enroute for updates and check ATIS if available around 80-100 miles out then make any adjustments needed for landing. There was a major magnetic shift a few years ago and a lot of runways were changed 10 degrees, for example RWY 09 is now RWY 10....same runway just different heading so keep that in mind. FSX will show the old number, the FMC will usually show the new one.

Do you have "show all variations" checked on the bottom of the plane selection page?