It is not normal practice to apply solder paste to through hole (multi-layer) pads. Can you use a paste mask to distribute enough solder paste to ensure that through hole components are soldered correctly if you IR reflow a board like that? Does the paste not just disappear into the hole and then get wasted when the through hole component lead is inserted?

To answer your question: You can add a solid region to the paste mask layer over each pad that you want paste applied to or you can edit the Footprints that then place the affected pads onto your PCB. Either way is tedious but the latter a bit less so. I haven't checked but is may be possible to do Find Sikilsr objectsvto select the relevant pads and then apply a positive Solder Mask expansion to them via the attribute in the right hand panel. If that attribute is not present, try adding it and then setting a value. * Always generate, download and check using gerbv, a test set of Gerbers.