This is how I do it: I only have one account on peertube.wtf. I usually discover content right here on Lemmy, in this community or in !peertube@lemmy.world. The channel directory is also a great resource for discovery.
When I click on a video that's not on my instance, I click Subscribe below the video, put in myusername@myinstance.xyz and click remote subscribe. It redirects to the correct place on my instance to subscribe/like/comment.
This way I've built quite a huge subscription list and have always around 30 videos in my watch later playlist.
When it comes to content discovery directly on PeerTube, I barely do it. Related videos aren't good recommendations most of the time. I tried the PeerTube Picks plugin for Firefox, it runs a local algorithm to recommend you videos. But I never discovered interesting stuff this way and it recently started to recommend me anti vaxx and other conspiracy videos, so I uninstalled it.