How to integrate several multiome objects

[sky5198]

I have scRNA-seq and scATAC-seq for two conditions (a control and stimulus). I have been trying to find a good tutorial but all I can find are tutorials that deal with one condition (ex: https://satijalab.org/seurat/articles/seurat5_atacseq_integration_vignette) . The scRNA-seq and scATAC-sequencing was performed in the same cell. My question is about the pipeline.

1. Do I process all of the control first (process the scRNA-seq object and integrate it with the scATAC-seq object), then process all of the stimulus, and finally integrate the control and stimulus objects so I can directly compare? or

2. Process both the control and stimulus scRNA-seq objects performing Seurat's integration tutorials, then process both the scATAC-seq control and stimulus together, and finally merge the combined scRNA-seq and scATAC-seq objects at the end.

I am fairly new to processing multiome data so any comments/ suggestions are helpful