You need to maintain two different versions of the same APK and create two different configurations for two CPU architectures.
Here is the flow.
1. Determine the CPU architecture for your existing APKs. The easiest way to do that is to get the phone model on which the APK is installed well, and find this model's CPU architecture (search the web for that!).
2. Rename your existing application so its name includes the CPU architecture, for example: WhatsApp (arm64)
3. Create an application for another architecture with the same package ID. Set the version to 0 and do not upload any file.
Click "Save". Headwind MDM will ask you what do you want to do, add a new application or a new version. Select "New application".
After that, select the configurations where this application should be installed. For example, if you are adding armeabi-v7a, then it should be installed on phones with armeabi-v7a architecture.
4. Download the APK for this CPU architecture from apkpure.com (Here is how to!) and add it to Headwind MDM. After the APK is uploaded, Headwind MDM will ask you to which application variant should this APK belong.
Select the appropriate one and click "New version".
Then select the configurations on which this variant should be installed.
Notice: if you simply upload the APK for another CPU architecture, Headwind MDM may not ask to create a new build variant, but it will just add as a new version of existing application, and you will not be able to manage CPU architectures.