With that network map, if you are setting those 2 port trunks up as trunks, then there really is no need to even use spanning-tree at all (I'd still recommend it though as users have a knack of creating accidental loops).
With just spanning-tree enabled, the common spanning tree (CST) is the active tree. If you have multiple switches that run MSTP, but you don't configure any MSTP regions - then every MSTP switch will consider itself the root of the Internal Spanning Tree (IST). There is no need to worry about this, just ignore it.
When you do a 'show span' all you need to look at is the CST.
For the edge-port setting, you should set PC's / Servers to edge-port... it is only switch to switch links that you should leave as no edge-port.
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