Is there a way to use tokens in order to trigger people that the email should go to? In this case, we would like to send internal emails to account/opp owners without manual effort.
Sure, if you have email fields storing those other addresses, they'll work in the "To other" box for a Send Alert flow step. Note this works for trigger SCs only (which is likely what you're already using).
This is usually accomplished using the OOB Sales Owner or Account Owner options available in the Send Alert flow step as Sanford mentioned.
If you don't have these fields mapped to your CRM and have custom fields, you can always select "None" and insert a token for an email address of your preference and it will work assuming that field is an email address. We actually do this as the Sales/Account Owner fields are not equipped to map to our assigned user fields in Sugar.
Another option is to build smart lists for each users geo and then use choices in the flow step to send the alert to each owner based on geo, but this isn't bulletproof as accounts/opps don't always stay with the rep managing a specific geo.
Hope this helps.