How would you go about changing themes or selecting KERNALS manually?
Same thing you did with the ROM. I use SPrecovery, so I rename the Theme/Kernel zip file to Update.zip, put it on the root of my SD card and install it from the recovery menu. I do the ROM, gapps, Kernel, Theme, in that order. It takes a little longer, but I'm in control of what happens and when it happens.
...and you find the themes and kernals online? Thanks again!
Yes, In each developers section on this site, there are usually links to Kernels and Themes that work with their ROMs. I'm a little unclear on which kernels are ROM specific, so I just stick with those recommended by the ROM developer. I believe themes are ROM specific, so check the section of the ROM you want for compatible themes.