Hi there,
From what i can understand you would want to get in the mind set of a layered animation approach. Usually you have a base layer then partial layer and then additive layer.
Additive layer can be used for head looks, aim offsets and general body posture adjustments. Creating additive reach “poses” which act as the delta from your base pose, then you manipulate the weight of those poses on TOP of the base layer. For reloading while running you will need to use a partial animation layer technique. In this method you “isolate” specific bones in your skeleton hierarchy which will play an override “reload” animation while everything below the spine (base layer) will play the running animation.
Your content will need to take this into account.
Cheers