Run default workflow (workflow A):
snakemake
Run non-default workflow (workflow B): snakemake --configfiles test3_config.yml
Modify parameters in the configfile to mix and match!
This is a tiny snakefile with a single rule per workflow, but this pattern should work for any number or rules and combinations, as long as the filenames produced by each rule are unique (and thus can be properly ordered by snakemake).
If your snakefiles start getting really large, you can try splitting them into smaller subsets, and using either include or subworkflows. I tend to keep rules associated with a single tool in small snakefiles, and then include/exclude them as necessary. Here you could have two files ruleA.rule, ruleB.rule, and then include/exclude them in the if statement where we define output_files via include: "/path/to/ruleA.rule", etc. See snakemake modularization for more.