TL;DR

You can use both of your phone numbers on Beeper as your iMessage aliases if you have them enabled as Dual SIM on your iPhone. Although according to Apple, you can have eight or more eSIMs saved on your iPhone, you can only have two active, those will be available on Beeper at the time.

Dual SIM on iPhone - Setup

In order to use two phone numbers through iMessage on Beeper, you have to set up the Dual SIM feature on your iPhone. For more information on this, you can review this Apple Support article: Using Dual SIM with an eSIM

Your iPhone > Settings > Messages > Send & Receive view should look like this:

Once your Dual SIM is set up, using your two phone numbers on Beeper is as simple as connecting your iMessage.

Your Beeper Desktop > Gear icon > Chat Networks > iMessage view should look like this:

Dual SIM on iPhone - How does iMessage on Beeper behave?

On Beeper Desktop you can select your default alias, all your new messages will be sent from this alias (phone number or email).

If someone to an alias other than your default alias, your replies will go through from the same alias you received your message to. Meaning that when using Dual SIM you don't need to worry about which number you're using on a conversation because it's going to be the same phone number/alias used on the first message of the chat (send or received).