I am not myself a conspiracy theorist, but even I find the answers to your questions painfully obvious, so I don't know why you'd start this thread.
If, hypothetically, the government created the 9/11 attacks, it knew that the planes would crash into the two WTC towers - there was no mystery about which buildings it would need to implode. At that point any competent demolitions expert could pre-place charges to bring the buildings down. C4, like some other explosive agents frequently used for civil demolitions, is not flammable and would not go off as a result of the impact or the resulting fire. By the same token, they would (or at least could have) install a tiered top-down detonation system that would allow them to start at any floor or group of floors (by placing, say, a set of charges at every fifth floor).
Again, I don't buy into the conspiracy theories, but surely if the government had the inclination and wherewithal to get the planes on target, the civil demolition piece of the plan would, relatively speaking, be small potatoes.