I already have an existing server with Nextcloud installed.
I noticed Mail-in-a-Box uses ownCloud, will it cause issues with Nextcloud?
Will I be able to create users within Mail-in-a-box and it will be created for Nextcloud two? and vice-versa?
It is absolutely inadvisable to mix Mail-in-a-Box with your own installation of NextCloud on a server. Mail-in-a-Box expects the machine it is installed on to be used for this single purpose and nothing else. Any changes beyond what Mail-in-a-Box does itself are unsupported.