depends on the server, my goal is to get multiple fedi apps running under a single login system so you can be the same account anywhere.

there is no playbook for this so you have to roll it yourself, the apps do support SSO through systems like LDAP so its entirely possible.

I'd say separate. You can only interact with the other instances through your instance, and while they use the same protocol, lemmy and mastodon are just fundamentally different styles of communication that don't mesh well together.

The instance(s) on which you have accounts dictate the interfaces you use to interact with the fediverse. If you find lemmy’s interface adequate for interacting with mastodon or vice versa, then you only need one account; but if you want to use different interfaces for different types of content, get accounts on instances that offer those interfaces.

I suggest separate accounts as you'll have a better and fuller experience. If you want to participate on both with a single account, I hear kbin has that capability.

Why would you not have multiple accounts? Even if it were pretty seamless to integrate everything into one, having multiple names is one of the benefits of free information exchange online.

For now it's better to have separate accounts, especially since Mastodon doesn't have sorting by upvotes, but it is entirely possible to have a software that does everything. We're just not there yet.

I'd also like an answer and insight into this question.

I've been thinking about this too. Only been on Lemmy a few days, so still only have this one account, but definitely considering creating others, for the same reason as I had different accounts on Reddit: to compartmentalize different interests and purposes. For instance, a technology account, a news/politics account, an NSFW account. The cool thing about the Fediverse is that you can also create those accounts on instances that match the purpose of the account, like tech on programming.dev, NSFW on lemmynsfw.com, etc.

Edit: I just realized now upon re-reading your question that it was specific to Lemmy vs. Mastodon. In that case, I would say definitely. I think the two systems are sufficiently different to warrant having separate accounts. I do have another Mastodon account. One on each system for now.