EDIT: After rereading your post, I thought about it a little. Try this first, and if it doesn't work, there are other solutions.
First off, navigate to the main FS folder. Highlight the Aircraft folder and right-click on it. Now click "Send to-->" and then "Desktop (create shortcut)". You now have a direct link to the aircraft folder on your desktop, which is a simplified way of doing what you wanted to do, without the hassle of replacing the Aircraft folder each time. I would also recomend you do the same thing with both the Gauges folder and the Effects folder. You could do it with all the folders, if you think you will eventually be needing to add more stuff like scenery and whatnot.
Now just do what you were saying, only you don't have to replace anything. Just drop it into the correct folder on the desktop. That SHOULD work. If it doesn't, read on:
!!!DO NOT REPLACE THE FLIGHT SIMULATOR AIRCRAFT DIRECTORY!!!This is important because there are numerous files in there that are utilized by FS as well as the aircraft to link to. The whole FS system is interconnected: NEVER overwrite files unless specifically told to by the download package creator, and even then keep your wits about you. Replacing ANY file in FS can cause some unknown instability that could crash either FS (crash to desktop, CTD) or perhaps your whole system!
Be careful . . .
There are download managers out there, for people such as yourself who do not want to or are unable to get downloads to work correctly for them.
Addon Manager 3.0 is payware, but I'm not sure of the quality. Take a look at it (bottom of the page).
Check out
FlightSim, as they have one that downloads directly into your computer without you having to do anything other than click a button.
Try
AVSim as well. There are several download managers there. You'll have to register and then do a search for them, so look for things like "Addon Manager" or "Download Manager".
And just so we make sure:
1. Open "My Computer".
2. Double-click the "C:/" drive.
3. Navigate this path in the folders "Program Files-->Microsoft Games-->Flight Simulator 9-->Aircraft".
4. Minimize the window.
5. Go find an aircraft you want to download on SimViation.
6. Click the blue link once.
7. In the box that appears, RIGHT-click on the blue link and choose "Save Target As . . ."
8. A "Save As" box will appear momentarily. Click the button on the left labled "Desktop". In the entry box just above the words "Compressed (zipped) Folder" enter a name that you will remember for the file to save as.
9. Click "Save".
10. Once file has completed downloading, find it on your desktop.
11. Open the file by double-clicking on it.
12. Expand the folder you opened in steps 1-4. This should leave you with two folders clearly labled on the Taskbar. Arrange them so you can see both and follow the directions you have already had.
All this SHOULD work. However, if it doesn't, I would contact tech support and see if they can help you, because it sounds like your system setting has gone awry.