Quick Review:
X contains all necessary genes as well as information about the female reproductive system.
Y contains all information about the male reproductive system. (males are an "upgrade" of females, more complex)
XX = Female
XY = Male
All human zygotes (life forms) start with female parts (ovaries, nipples, etc.), with information only from the X chromosome. At some point, information is read from the Y chromosome (if it's there) and the zygote develops male parts (ovaries become testes, etc. It's science, stop laughing at the words).
Wikipedia article which may help.
Yes, most genetic modifications deal with changing the DNA sequence of genes, the actual A-T-G-C stuff.
And yes, as far as I know, it's hard to change genders of fertilized eggs.