How to specify a via should be plugged to prevent solder wicking?
With my usual Chinese proto house it's specified on the order form, and adds about $150 US to the cost for 5 100x100mm boards, also adds a few days to the lead time. 

If your board house does not have that,  you can put it in the readme file or fab drawing along with material, stackup etc. 

If you want some of the vias plugged and not others, you'll have to talk to them and find a way to differentiate them if they agree to in fact do it. I suggest making the plugged ones unique in some way (eg. slightly different size to the rest).