I am starting to work with some single cell sequencing data and I am trying to get my head around what the best pipeline is.

I have 6 samples in total, 3 from control and 3 from a treated group. Of each, 2 were done with a 10x multiomics kit (scRNAseq and scATACseq) and the other is only scRNAseq.

I was going to align the multiomics samples using cellranger-ARC and the other sample using 'vanilla' cellranger, then process everything in Seurat.

However I'm not sure if

1. that's the best way of proceeding
2. how do I go about putting everything together (and whether it is possible). I'm going to align samples separately and then use cellranger aggr or cellranger-arc aggr. Would I then be able to import everything onto a single Seurat object or what's the best strategy?