Hammer. I think you're a tad confused here. Renaming the FS2002 root directory folder hides it from the setup install program on the CD. I suspect you didn't rename it correctly or renamed the wrong folder. Here's one way of doing it.
First find the FS2002 folder.

Rick-click on the FS2002 folder & select the Rename option.

The text will be highlighted in blue ready for editing.
Type the new name in the box. Any name will do providing it's different.
I used FS2002 Old.

Click on a free space in the window to finish the process. If you don't, the name might not change. Make sure it has the new folder name.
Now exit Windows Explorer & all other open programs. Insert FS2002 CD-1 & select Install. Let it install to the default path. When it's complete you will have 2 separate installs of FS2002.

WinZip is used for compressing/extracting zipfiles & other compressed files. It's not used for editing files. The MDL would not usually be edited. The AIR file can be opened in an FD editor like AirEd from the Design Utilities section. Other files like Aircraft.cfg & Panel.cfg can be opened in Notepad or other text editor. I don't think you will need to do this for a while. Let's get your FS2002 straightened out first.