There are a couple of different ways to organize your custom tracking domains.
Based on per-business basis.
Use a single custom tracking domain for multiple sending accounts. This would make sense if your primary domain is old/warmed up. If you're running a lead agency, this is what we would recommend.
Based on associated domain for the email account.
If you had [email protected] and xyz@ second.com, you may use track.first.com for all email address associated with first.com. This approach would make sense when all of your domains are new, or if you're experimenting with a new campaign that could potentially have a negative impact your reputation. By creating separate groups, you can minimize the damage from a bad campaign.