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,

Lee

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.

In short, no it won't.

If you're following best practices in terms of opt-in process, are following good list hygiene practices, AND you're providing engaging content, then your sender reputation score should go up over time with consistent sending. Whichever of the two domains had the most engaging content and consistent sending patters will enjoy the best deliverability and inbox placement. If you have certain content that is not as engaging as other, mixing it up helps get the less-engaging content delivered.

If you separate the engaging content from the not-engaging content, then one will enjoy good deliverability and the other will not. Deliverability and spam filters are ALL about engagement. There is no cheating them or tricking them.

Its important to remember new domains should be "warmed up" first to give the email service providers time to see you coming. Send regular small, incremental batches of highly engaging content. If the email confirmations are opt-in confirmations, then these should grow organically as your list grows reducing the need for a warm up.

Feel free to schedule a call -- I can give you more specific help if I know more about your situation.