NPCs, problems with making npcs Options

[scapegoat]

i have been gm for the only a couple of runs. And i have a few problems
1. the players always challenge what i say. this is here is the most annoying not only does it slow down my runs but players often forget what they are doing and start agruing between themselves as we try to figure out the exact rule

2. NPC...i cant seem to make an npc seems important most of the time ether the players kill them or they ignore them.

3. this is the last, combat for us seems to be i attack....roll so dice and boom hey the enemy is dead...which i cant seem to find a way to make it a challenge to my players. so far all them seem to do is cast improved invisibility and hey now no one can see us so now i run around killing everything.

so here are my problems. think you guys can help my out here?