How do I run two sequences at once, without overwhelming my subscribers?

If you have an existing subscriber already in the midst of your Welcome Sequence, and then they opt in for your ConvertKit Cheatsheet Sequence, you want to pause the Welcome Sequence until they've completed the Cheatsheet Sequence, is that right? 

The best way to achieve this is to set up the following: 

Create an Automation that, when a user is subscribed to the Cheatsheet Sequence, you add a tag. I'll call it "Cheatsheet Sequence." 
Create a second Automation that, when a user completes "Cheatsheet Sequence," you remove the tag "Cheatsheet Sequence." 
Exclude the tag "Cheatsheet Sequence" from your Welcome Sequence. 

Setting it up this way allows you to exclude only the subscribers that in-progress. If you excluded the entire Cheatsheet Sequence itself, they would never return to the Welcome Sequence, because a Sequence is not removed from their Subscriber profile.