My solution so far: search on browse.feddit. Copy complete link. Go the web interface of your instance. Go to search and there select search ALL on ALL instances, enter the complete link. Click the found result and subscribe from the sidebar.
I think the proper behavior would be that two instances are federated, a user would be able to see all communities in both.
It's going to be especially hard for users on a small instance to find content if they, or some other person on that instance, has to search for it first.
If I type "!coffeeaddicts" into the search bar, it should show all communities in all instances that are federated with my own that match that query. A person running their own instance would have to search every single community and wait however long for it to populate.
A web browser, yes, but you should be able to use your sopuli.xyz account just fine. For example, to get to the Jerboa community we're having this discussion in, you would go to the URL https://sopuli.xyz/c/[email protected] in your web browser. What that does is basically tell sopuli.xyz to show you the community named "jerboa" hosted on the domain (instance) named lemmy.ml. Without the @lemmy.ml, it would look for /c/jerboa on sopuli.xyz, and get a 404 because it isn't hosted there.
If you're signed in to sopuli.xyz on that web browser, you can subscribe to the community from there, and then you would be able to get to it from within Jerboa. My account is with beehaw.org, so if I wanted to do the same, I would go to https://beehaw.org/c/[email protected]. It's a bit weird, but not that complicated, and it will quickly seem normal once you get used to it.
All that said, one thing I've noticed is if a community from a different instance than the one you're using has 0 posts, it will 404 if you try to go to it from your own instance, and it also won't show up in a search within Jerboa. For example, [email protected] has 0 posts as of this writing, and will 404 if I try to view it from Beehaw or sopuli; it only shows up if I view it directly at lemmy.ml/c/animanga, which doesn't help much since I don't have an account with lemmy.ml.
As a workaround, if you login with your account on the web site you could subscribe to your desired communities and then they'll show up in jerboa.
To view a community on another server from your server, in the search box put "[email protected]" for example [email protected] and after a few seconds it should show up and then you can click on it and subscribe.
The easiest way is to go to your instance's search bar and look up "[email protected]", in the case of this community. This should make it show up even if it wasn't added to the instances "index" (I'm also new here idk the terminology all that well), as long as both instances are federated, which they most likely are. But yeah it doesn't work on Jerboa yet. I used that to subscribe to the communities I wanted
I put "[email protected]" in the search area, it took a while (a few minutes), but eventually it showed up. I think it takes a while to sync/federate in the background if you're the first person on the instance to subscribe to that community.
Edit: nevermind, this doesn't seem to be working when I tried again... :-/