Plugged vias are either filled all the way through or can have the holes partialy filled (plugged) with solder resist (usually a film type, not LPI resists).
Plugging with solder resists has two camps of followers one who say you can do it, the other camp that says its bad... I've used both methods and had no problems, so I am neutral on the subject...
For via in pad technology you require filled vias, and then plated on top, filling vias involves more work than plugging them, but can have certain advantages, though if you dont require it dont ude it as it costs lots.