IEEE Conference Paper: Different Author Blocks, Different Information?
In the IEEEtran_HOWTO (available in the template you link), they seem to actually mix a bit between the number of affiliations and authors. They actually write (Section IV.2): 


  If there are more than three authors and/or the text is too wide to fit across the page, use an alternate format:


which corresponds to the second format you put. So, basically, there are three possibilities: 


You have 3 authors or less, in which case you use the first format. If the first and third authors are from the same affiliation, then you can just repeat it, to keep the author ordering. 
You have more than 3 authors, but you can split the list of authors in 3 affiliation blocks. In this case, you use the first format. 
Otherwise, you can use the second format, even if you have only two affiliations, but the author ordering is somehow interleaved. 


In case of doubt, you can use the format that makes sense to you, you will be contacted by the editor if there is any problem.