There is no "best way" of installing Linux. All that you have to do is delete and existing FAT32/NTFS partition and have some free unpartitioned space for the Linux installer to use. Installtion procedure will differ from distro to distro.
You boot into Windows and use fdisk /mbr. This will restore your Master Boot Record.
Then you can boot from the first installtion CD, get into the rescue mode, use Linux fdisk and delete the linux partitions.
I have posted the commands somewhere in this forum. Please search. If you don't find, let me know.