"My question is, what is the appropriate autoqos command for the access ports to retain or to honor these markings? Is it simply auto qos trust? Obviously some of the markings are for video too.. Is anything different needed on the uplinks?"
That's hard to answer, with the information provided, because AutoQoS has varied, over the years, across different IOS versions. QoS features vary per platform too. Lastly, there's the impact to consider AutoQoS may have upon your other traffic. Uplinks are usually impacted by the activation of AutoQoS, which should enable QoS globally (at least on older IOS version, by default, QoS features are often disabled on most network devices).
An interesting statement, which is bolded in your reference is "This leads on to one important statement on Skype for Business QoS: QoS will only work in Skype for Business IF the network it runs on has been properly configured to support DSCP." Again, though, realize once QoS is enabled, it applies to all traffic, so you really want a QoS policy that matches your services goals. AutoQoS might be used as part of such a policy, but personally, I feel it's better not to use it. (BTW, the QoS model the later variants of AutoQoS uses is worth understanding.)
