It is possible to run 3 different AmpliSeq for Illumina designs each with barcodes on the same sequencing run. However, your target amplicon size and required coverage must be achieved in a single run.
Yes, Illumina recommends spiking in PhiX for low diversity samples such as Jurkat. Follow the appropriate denature and dilute guide (≥5%) for your sequencing system.
You can manipulate coverage by increasing sequencing throughput (eg, a larger flow cell output or sequencing platform) or reducing the number of samples pooled per run.
On-target bases shows the percentage of total sequenced bases that map to target regions in the reference genome. This metric reflects the percentage of bases from amplicons that a) were designed, synthesized, and pooled and b) generated sequence data mapping to the target regions.