Hi,
I'm not sure I understand clearly what bothering you, but here's my answer:
I Altium VIA stitches (clings) to the polygon or trace beneath them automatically. If you place VIA on two different traces (they cross each other in different layers and are conected to different nets) pop-up menu will appear where your can choose corresponding net. You can connect any VIA in any time to any net using right click menu>propetis>section Propetis> parameter Net (drop-down list).