1) Resistance does nothing by itself, but there are lots of cards that key off a companion's resistance. Remember, each companion's resistance is reduced by 1 for each burden on the Ring-bearer.
2) Threats are placed on the dead pile; you can't place more threats than there are companions in the fellowship. When a companion or ally is killed, all of the threats are converted into wounds that the FP must put on his companions.
3) You put the twilight cost for the sites in the twilight pool when you move to that site.
4) You use cards that take control of sites to take control of sites.
5) Fortifications do what they say they do.