Yes if you reinstall WinME, you are correct, it will overwrite the linux bootloader. But it is possible to reapply the linux bootloader.

The bootloader you are using is most likely GRUB. Here are some other posts where I help people reinstall the grub bootloader.

http://www.knoppix.net/forum/viewtop...ht=grubinstall
http://www.knoppix.net/forum/viewtop...ht=grubinstall
http://www.knoppix.net/forum/viewtopic.php?t=19793


If you are using LILO, then read this
http://www.knoppix.net/forum/viewtop...?p=86429#86429