Currently we have two domains and separate traffic between them but are still having issues with email confirmations getting caught in spam filters or services.
Agree with Lee's responses so I won't reiterate his points.
Additionally, the use of multiple domains is a strategy to ensure that deliverability for your transactional/product/account related messages isn't affected by any sales/marketing related email communications which may be sent through a different domain like a .co or a subdomain.
Gaming the system is temporary. Seems like you need to repair your IP/domain reputation and change your strategy for copywriting, send frequency etc.
ps - make sure you have DKIM and SPF records set up.
