If I have a licensing code that came with a CD can that code be used for the app as well when I file versus having it deducted from my returns? Trying to avoid paying twice

Sorry, but no.  The license code is specific to the Desktop (CD/Download) platform.  If you choose to file using the mobile app, it is totally separate from the CD program that you've already purchased.  

https://ttlc.intuit.com/community/tax-topics/help/why-am-i-being-asked-for-a-license-code/01/872421

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If you bought the CD Desktop program why are you using the  Online version or App?  The Desktop program has more features than the Online version and can do more than 1 return.

If you don't have a CD drive you can download the program.  Otherwise you should return the CD and get a refund then you can pay for the online version.