Right now, a campaign using custom emails can only use a single email. If you want to use more than one you have to create multiple campaigns, which then means that if all your users are in one group (while being broken out into other groups for other purposes) then they will receive ALL phishing emails.
However, if you use the random campaign which pulls from the non-custom emails then it's far more obvious that they are phishing emails - the entire point of customizing them is to ensure that the 'hard' emails really ARE hard. Campaigns using custom emails need to allow for far more than just a single custom email in order to make them effective (both the customization function as well as the difficult phishing campaigns).