Can the cyber eyes basic set be installed in a cyber skull?
No
Cyberskull is just basically a metal plate "shell" around your head.
It does not replace your eyes, ears, brain etc. and it doesn't really come with any hidden compartments to hide stuff in.
If no, then how does one get stuff into a skull because the capacity is so low?
The capacity is there so you can enhance the skull with up to two points of armor (basically making a helmet worn on-top of your skull twice as efficient).
If you don't want to use it for armor you could still fit a commlink or an ultrasound sensor in it i guess....