The problem with BerryBoot is, that it actually mounts the operating system(s) as IMG-files, and stores all the changes in a seperate part of the sd-card.
Therefore you can’t change the /boot/ folder of your operating systems.

BUT: you can however modify memory split through the GUI of BerryBoot! If you can figure out where this information is stored, you can probably add the neccessary lines for overclocking there too!