How to submit a manuscript in two parts?
The answer to this is "it depends." Some journals do not approve of "series" of papers, expecting that each submission stands on its own. Others will publish extended series of articles (one such series had at least ten entries). So the question of what to do depends on how appropriate the journal in which you want to publish is for the content you're writing about.

If the journal you're publishing in allows it, then there's no problem submitting two manuscripts at the same time, and that's probably the best way to do it, because the related nature of the two manuscripts is much easier to assess. Waiting to send in the second one doesn't help.

As far as the appropriateness is concerned, my first four papers were published as two pairs of manuscripts, so there's nothing wrong with doing so to keep the length of the individual manuscripts reasonable.