Okay so I did some lab on this and here is what I found:
1. Layer7 rule set defined on Traffic Shaper with Skypeout and SkypetoSkpye with option of queue and queue called qSkype.
a, Set qSkype to have 10% and real time 10% bandwith on LAN and WAN.
b. Placed Floating rule at top of rule set for TCP / Layer7 chosen. Used WAN and LAN interfaces.
c. Killed all session states from test PC.
d. Tested and I can see qSkype fills up as does qHTTPSteam. Placed Skype test call and it worked. Ran speedtest and it worked once but then failed 2nd time and browsing was slow.
2. Replicated above but removed Floating rule and placed on LAN rule interface.
a. Left wildcard of any host in.
b. Same test results as above.
3. Replicated above but made changes on LAN rule for specific IP of machine I was using.
a. Tested with same results as in #1.
So it would seem that the Layer7 part of this is not working very well or is fully implemented as I would expect it to use DPI to see the packet was a skype packet and apply the rule rather than applying all the rules to it.
Since you can define the incoming connection for Skype you would be able to shape calls coming in for it but since Skype uses any port above 1024 TCP , kind of hard to shape it unless you can get PFSense to see the program calling it and recognize it via the Layer7.
Like I said , never used Layer7 before as at LAN's not really needed. This is just what I have found in some early testing.
If anyone else has any other ideas on how to shape Skype , I would be interested in hearing them.