Oh, now I realized I overlooked the OP wants shorter batts. Sorry, I tacitly assumed the OP was going to have some custom made extension or external battery pack. In this case it is as Oliver says. By combining two shorter batts there will be some place wasted between them, which could be used for more capacity of single cell instead. In other words - no reason to do it like OP asks IMO.If you use two 18350's in series you will be inputting 7.4V instead of the 3.7V you need. Also two 18350's will be 5mm longer than one 18650. I recommend you stick to the recommended battery type.
This wouldn't benefit you in any way as even if you had two 18350's in parallel the capacity would still be less than a single 18650. If we are talking about protected cells.
Edit: Was in process of writing this at the same time Radim also he wants to use 18350's. Two 18650's would be significantly too long for the host.