however, I quetion is about navaids.

I look at 'stock' airports and notice that the ILS symbols are very wrong. The ILS cones are on the opposite ends and the smaller ILS cone is off the R/W all together. I have seen questions about the ILS and the "Having to correct before landing" but I wonder if I move them in AFCAD to the proper place will this take care of the ILS problem and bring me to the R/W lined up with center?

Madcat I think what you are seeing is the backcourse ILS this is 180 deg. opposite of the actual ILS if you click on the arrows then click properties you will notice the backcourse box is checked AFCAD does not show the ILS as being down the center line IF you are having trouble with a default airport ILS you might want to make sure you have the correct frequency and the correct course heading set on nav1 8)
AFCAD does not give you the option of where to put the ILS it knows where it has to be  by the runway number. All runway number are the heading you fly in order to land on them + or - a few degress for magnetic varation. EX in order to land on runway 7 would you fly a heading of 070 + or - a few degress.. 8)