Q: How do I let the journal know of two first authors in case their submission system does not allow this?

It’s a bit odd that the journal’s submission doesn’t allow this. However, what you have thought of is quite smart. :-) Apart from that, or rather, before that, you could check this with them through a presubmission inquiry. That way, they might be able to show you how exactly to do this before submission itself, rather than you having to follow up with them after submission. The issue could be due to a bug, a display problem, or something else. Hopefully, it should get resolved. Otherwise, it could lead to an authorship conflict later – and that would be a bigger issue! :-)

All the best for the inquiry and the submission!

As you are on the verge of submission, you may find the following resources helpful:

• Dos and don'ts for a great cover letter
• What are the first things journal editors look at in a submission package?
• Learn about final checks and revisions before manuscript submission [Course]