Amplicon projects use nextgen sequencing technologies to deeply sequence PCR products. Typically these PCR products are generated using universal primers that target ITS regions or 16S/18S ribosomal RNA genes, with the goal of using these markers to characterise the number and type of species found in each sample.
In contrast Metagenomic projects randomly sequence genomic fragments found in biological samples. These random fragments are then assembled and annotated to reveal molecular and metabolic pathways that can help define the functional properties of the community/sample.
This depends on the complexity of the microbial population in the sample. It also depends on the taxonomic resolution (order or species) that you require. If you expect only a few species or you are happy with more broad classifications you can include more samples on the sequencing run and visa versa. However, as a general rule we would warn against including more than 100 samples on a single MiSeq run.