If you create new custom activities after the installation of ActivityTools they will not be shown in the activity type drop down and in the NEW ACTIVITY menu of ActivityTools.
This article shows how you can make them available.
To make the new custom activity available, please open your Dynamics 365, navigate to Settings and select ActivityTools, like you can see below.
After reloading ActivityTools the custom activity will be available like you can see below.
Figure 5: Activity type drop down with custom activity
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