If I have a custom compiled kernel, will it get updated bu pacman?
If so does it respect my .config file for the kernel I compiled?
This can only happen, if the names of the kernel and the config are different from the normal one.
But you can set the kernel on "Hold" in /etc/pacman.conf, so at least you are asked, if you want to upgrade it.
If it has a different name you can have several kernels.
Isn´t it wonderful?
... and no, it doesn't respect your .config file.