Is there a way to prevent Credit Memo's from automatically applying to a payment that you are creating?

You can turn off the automatically apply credits feature, Rafi2. I'll guide you with the steps.

This will stop the system to automatically apply the credits or unapplied payments to the open invoice. Here's how:

1. Click the Gear icon.
2. Select Account and Settings.
3. Go to the Advanced tab.
4. Click the Pencil icon in the Automation row.
5. Uncheck the Automatically apply credits box.
6. Click Save, then Done.

Although, if you've turned off the feature already, you can still see the credit or unapplied payment when you record the payment manually. If you're not going to apply it to the invoice, ensure not to select the credit.

I'll share the article on how to enter and apply credit memos and delayed credits in QuickBooks Online for future reference. 

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