I'm thinking of sending my runners to do a run at the Tsimshian / Salish border circa 2059 (so the full war hasn't started, only light border skirmishes). My question is, what exactly does this mean? Does the military have outposts scattered in the forests and small bases in various villages? Are they going to encounter patrols around in the woods? Are they gonna be shot at? Can they go about freely, or do they have to be careful avoiding outposts and known patorl routes?

Borders are mainly sensors. I'd say with the countries ramping up toward war, you'd have a lot of patrols, as well, though. The chances of the PCs encountering one should vary directly with how subtle they are being (ie, wilderness survival skills or not and specific attempts at stealth).