an invitation to eat as much of whatever is offered as you want and take some home with you. the phrase may come from a time when inviting travelers into your home to share a meal was more common. it was considered polite to eat your fill but not to also fill your bag with food for later. the invitation to "fill your boots" would be permission from the host to do so.
host: there is more here than we can all eat now, feel free to fill your boots.
guest: thanks mister, that's generous of you.