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.
There are a couple possible reasons why your emails are being caught in filters:
1) The behavior towards your emails of most of your recipients is indicating to spam filters that it's spam. This could mean actively marking them as spam, or even just deleting them without reading them.
2) The text content is algorithmically associable with spam. This could mean you have a word or collection of words in your emails that is correlated with spam emails, or that you don't have certain words, like the person's name, in the email.
Regardless of which problem it is, creating a new domain will at best only temporarily get more emails through. You have to address the two possibilities by doing the following:
1A) Make sure you have an easily accessible 'unsubscribe' link in your emails, and that clicking on that link either directly unsubscribes them, or takes them to a very very simple interface to unsubscribe with.
1B) Make sure you aren't sending your emails too frequently, causing people to get annoyed to the extent of not bothering to click 'unsubscribe', and clicking 'mark as spam' instead.
1C) Make your email content actually be something that recipients want/are interested in. You want as many people as possible to actually be opening it instead of deleting it unread.
2A) Go through your email content and making sure you don't have too many words or phrases associated with spam. For instance, "As seen on", "Earn $", etc.
2B) Personalize your emails to the degree possible (if you have names, put the first name in the subject line).
Note: your IP address may have been marked as a spam source, so even if you do the corrections above, it may take time before they start un-marking you, so if possible, see if you can start sending from another IP address when you're ready to implement your changes.
best of luck,