Flashtool is used only to push in a kernel. If you want to change your kernel you need to use flashtool. Some ROM works on stock kernel. In that case you wouldnt need to change the kernel or use flashtool. Just use recovery. But if a ROM specifies the kernel that you have to use, then you do the following.
1) download flashtool from http://androxyde.github.com/Flashtool/
2) download the kernel you want which is a ftf format
3) install flashtool in a particular directory
4) move the kernel file (ftf file) to the firmware folder in the installed directory
5) run flashtool
6) click on the flash button (the thunder like icon)
7) choose flashmode. A dialogue box will open where you can see the list of kernels in the firmware folder
8) choose the kernel you wish to flash and click OK.
9) It will tell you to unplug, reboot and reconnect holding the back button. Do so.
10 Flashtool will flash the kernel into your phone.
Edited by emoninet2, 11 June 2012 - 07:54 PM.