Speaking in general terms I think a siege should consist of 3 stages:
1. Preparation and taking hold
You prepare the siege by moving those things you need in favourable position. You might want to have gear available in the next NPC city for example. You also will have to sort out the logistics of the "special" resouces. Those would be "siege timber" and "stone boulders" etc. I think you should be able to prepare some of that, but it should be something that is hard to hide. Once wagons are introduced they would be good indicator. Something that make it very clear to someone watching that you are not transporting wool.
This is the phase were the aggressors can either be sneaky or try to take control of the area. The defenders can be vigilant, or asleep.
2. Siege camp
The attackers build a siege camp. I imagine a structure that works similar to how the original housing system worked. A fairly big foundation (like a flat area with a ditch around it, maybe stakes etc.) and a chest to have resources in. You build it like a house, you can prevented by being killed, getting your resources stolen or even someone bringen siege weapons and shooting your camp. I think this is a part where special resources COULD come in.
I think it would be cool if character with certain skill sets can make those on the spot and if there was some kind of group effort involved (like lifting big logs or something, compareable to the old battering ram). Basically good organisation should be rewarded, compared to sheer numbers.
3. Battle
The siege camp stands and you build siege engines. You push/drag/teleport those towards the enemy and begin the actual attack. I´m not the one to provide any details on this. Generally I feel guards should not play a big role and good organisation should be rewarded on both sides.
I have not assigned any time frame to each phase because that is up to SV. There is a lot of factors to consider. I think in terms of actual game play the 1. and 3. phase will be the most interesting, while the siege camp will be mostly about the tension of all your efforts possibly being reversed.
I think regardless of implementation this system will favour the defender, just as a siege window or declaration will. I think the flexibility of it will allow for variation on outcomes with small groups though.