How to use overlay/floating apps in Android 6.0 conveniently?

With the latest update in marshmallow devices , now we get a 'screen overlay detected' dialog which doesn't allow us to allow or deny any permission. I also Googled about this issue and i found out that the 'pie control' app installed in my phone was causing it and it was a part of the update that screen overlays should be disabled while granting permission.
Now i just want to ask that how is it gonna be possible for marshmallow users to use screen overlay apps as we would have to disable them every time any app asks for any permission :| :rolleyes:
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