If evolution is true, how do all organisms have varying amount of chromosomes?
A mutation is a general term referring to any alteration of a nucleotidic sequence. It includes small mutations like indels (insertion or deletion of a single nucleotide) and substitutions, or bigger mutations such as e.g. chromosome fusions, whole chromosome duplications, whole genome duplications and gene deletions. So yes, some mutations do change the number of chromosomes (and ploidy number).

If you are interested in a very short and very introductory course to evolutionary biology, consider having a look at Understanding Evolution by UC Berkeley