You will be able to send from the top level domain of your company (e.g. as john@company.com) by purchasing and configuring a Private Domain on your company.com domain. Assuming you already have your SAP in place on e.g. marketing.company.com. Those need to be within same top domain as DMARC will otherwise fail.
As in most cases for SAP, the subdomain in delegated to Salesforce name servers, and all DNS configuration is managed by their team. This is obviously not possible with regards to you top domain, so you will be provided with a set of DNS records to be updated in your existing zone of company.com
Also managing RMM in SFMC will not be possible, as MX records for company.com already point to your existing mail servers
For each BU you can deploy one SAP.
For each SAP you have, you fill in a separate form.
Last time I checked, the SAP form asks nothing about Dedicated IP.
The standard procedure here is, one Dedicated IP will be set up automatically with the SAP, for the BU whose form you fill out.
That is UNLESS you specify in a remark that you want something specific about the setup with that one IP. (e.g. you specifically do not want to have a dedicated IP but stay on a shared pool).
So - each SAP form deploys one dedicated IP pretty much "automatically" unless you object.
Now you want a second IP in the same BU, and have a dedicated IP purchased:
Open a separate support ticket. The way to alter anything about IP setup is through a support ticket, I believe in the Deliverability subsection.
The standard behavior after a second IP deployed is that the default "delivery profile" rotates the two, but you can specify that other delivery profiles use either IP exclusively and assign them for e.g. transactional vs. commercial send classifications.
There is relatively high flexibility with Dedicated IP setup also post-deployment, like, you could make two BUs use the same IP etc. - all through support.
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To be clear:
Sending from two separate subdomains in the same BU is not possible unless you purchase an additional Private Domain for sending.
Private Domain doesn't cover all SAP features (when it comes to branding), but can be set up in the same BU as an existing SAP and gives you another sendout domain to choose from.
With just two SAPs and no private domain purchased, you have to split your two subdomains to separate BUs. This is notably NOT as flexible as the IP stuff. One BU - one SAP is a hard rule.
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RMM settings are done inside the BU as a fallback, and you can override the default setting by Sender Profiles. So this is completely unconnected to the IP setup or the SAP form. Simply defining and using separate Sender Profiles for commercial / transactional should cover your requirement.
I would recommend researching the docs at https://help.salesforce.com/s/articleView?id=sf.mc_es_reply_mail_management.htm&type=5 first.
If you need specific details then I would open another question to keep some focus.
Best Answer
Yes, we multiple sending domains in our single instance. When we want to add a new one we have to order a "Private Domain" which is a small additional cost for the domain to be authenticated. They will send you the instructions to delegate the DNS to them.
Thanks Susan