If a baby is born "bein hashmashot" how do we count the days till the 8th for the bris? For example, if it's bein hashmashot Sunday evening, will the bris be the following Sunday or following Monday because you could say that since it's after shkiya that it's the following day?
The halacha is that bein hashmashot is safeik yom safeik lailah - doubtfully day or night.
In your example, bein hashmashot of Sunday evening is either Sunday day - in which case the brit is the following Sunday - or Sunday night (i.e. halachically Monday), so the brit would be the following Monday.
Because a brit cannot be performed earlier than day 8, but is valid if is performed after the eighth day, the brit is held on the Monday (possibly day 8, possibly day 9), rather than on the Sunday (possibly day 8, possibly day 7).
(Source: Shulchan Aruch, Yoreh Deah, 262:4)
The major exception to this rule is if the baby is born bein hashmashot of Friday night. According to the logic presented, he ought to have his brit on the following shabbat (possibly day 8, possibly day 9).
However, the rule is that a shabbat brit only takes place if it is certainly the eighth day, not where there is a doubt. For this reason, the brit in this case happens on the following Sunday (possibly day 9, possibly day 10).
(Source: Shulchan Aruch, Yoreh Deah, 266:8)