When I load a sorted bamfile and a fasta file, should I automatically see the coverage graph and SNP call track?


No, the coverage and SNP are in a separate data file.

Instructions to create this file:

There are two recommended file formats depending on your visualization needs:

1) TDF: this file format is the most space efficient and fastests, however, it only has coverage information.
see the TDF section in the link above

2) pileup: this file format has both coverage and diversity information. The diversity information is required to display the SNP track.
see the SAMtools pileup section in the link above