Eggs come from Pokestops, so as long as you're not maxed out on eggs in your inventory the bot will grab them if you're looting pokestops. The bot will hatch them for you and any pokemon that come out will be kept under the same transfer rules that you have setup to apply to caught pokemon.
The main problem here seems to be that you'll always be collecting eggs way faster than you can hatch them. Eggs are pretty common from pokestops and you can only hatch one at a time without spending real money on more incubators.
