Since feb’2015, It is mandatory to have 64-bit support in your Marmalade App.
In order to deploy a 64-bit compatible .ipa, you need Marmalade SDK 7.5 or higher.
First, build your application using GCC AARCH64 Release, instead of old GCC ARM Release.
Then, when Marmalade Deploy Tool opens, select “ARM+AARCH64 GCC Release” (see screenshot below)
In the next step “Stage: Configuration – Platform selection”, select “iOS fat” as the platform.
Rest of the steps are the same. Click on “Deploy All” to run the deployment process. Note that iOS-native extensions must be also recompiled in a Mac running iOS 8 SDK or higher. Else, ld will ignore the .a files and extensions won’t be linked to your .ipa. If you also need to link your 64-bit iOS extension see this post.