So does anyone know if getting "seen" by a weeper counts as an alert? I've been trying to make sure I don't get seen by the guards for sure but I'm not sure if weepers count. Anyone know?

I don't even think getting seen by guards counts as an alert if you get them before they actually activate the alarm, so I would say you're fine if weepers see you.

@SlashDance: I think "alerts" and "alarms" are two different things I say this because in the first mission I managed to set off the base alarm after tranquilizing the mark although i was never seen in the process. The alarm was sounded but the results screen gave me credit for never being spotted.

A weeper seeing you does in fact count as being seen.

Good to know !