Below mentioned are a few ways to manage and prioritize your sequences.
You can set up a new email account within Uptics for the less urgent sequences, and allocate that account accordingly in the sequence settings for sending.
Filter the 'Email' and other tasks under the 'Inbox' - you can filter tasks generated from the respective sequences, by 'Name' or 'Description' under the Sales Inbox page.
If your task names or descriptions are different among your various sequences, that would allow you to differentiate them by running a filter and saving them as a 'SmartList' in the Sales Inbox.
For 'Email Replies' showing up in the Sales Inbox, currently, there is no way to differentiate which address the replies were to without opening up the Contact Card and checking the email string. This, however, is something that we have in our backlog for future development.
Another option, aside from sorting by task name/description as mentioned above, would be to add an additional 'User' and have your high priority sequence sent from a connected email under 1 user profile, and your low priority from another. The Sales Inbox is a shared inbox amongst any connected email accounts you have under a specific user account, and thus the only way currently to distinguish different task/email types is by the static filters at the top of the inbox. This includes email replies, tasks that are assigned, etc.