I operate the same way as you do, except that my company is platitor de TVA.
you will need to register in the ROI registry, if you have not done that so far.
also, the bank account registered as payment method with upwork needs to be your SRL's bank account.
I retrieve my earnings from upwork to that bank account. the money send by upwork will hit your company's account in 5-7 days. they send USD, but you cash in EUROs. so you lose a bit because of the conversion rate.
if you want me to, I could refere you to my accountant. she services other freelancers, as well.