I was going to post this a couple of weeks ago but Colin Meade has answered my questions in a very informative post.
I must remember to follows Colin’s steps in IIS.
After provisioning my BizTalk service in Azure I proceeded to refresh my developer machine with the the new WABS SDK and runtime.
I installed the new BizTalk services SSL certificate in my personal store. I followed the SDK install instructions and had everything installed except the run time and I continued with the install.
I was not sure what SSL certificate to use at step 6, the one I had just imported was not available in the dropdown. I found my machine had two other certificate in the dropdown so used one of these.