The manual is indeed very scant on virtual comm port details.
I use Logger32 as my main logging programme and have done for years, it is the best logging programme on any platform by a long, long way. The only other logging programmes I use are N1MM and latterly DXlog.net (I switched to DXlog recently) and the qso details are imported into Logger32 at the end of every contest which allows me to keep track of everything.
I don't think anything is particularly Logger32 specific, I have noticed that on launching N1MM or DXlog.net I sometimes have to change band using the logging software and it's keyboard shortcuts for things to sync up and thereafter all works fine. I should mention that when using Logger32 I am seldom changing band using Smartsdr, I am usually changing band by clicking on a spot on one of the several bandmaps I have open or a spot in the tracking window.
Smartsdr emulates a winkeyer, you simply create a port in Smartcat and define it as a winkey and then point your software to it. I've attached a grab of my Smartcat winkey port settings along with grabs of how I have configured N1MM and DXlog.net to use it, it's a bit jumbled up but you should be able to work out which is which. Incidently Logger32's CW machine works just fine with it but I don't use it as it duplicates the functionality of the CWX features that already exist within Smartsdr.
73, Frank GI4NKB