Small note on that, as described in this blog post: Make sure than when you perform the concatenation, you have the first b=0 AP volume as the first volume in the concatenated SE-EPI series, not the other way around. This will ensure that spatial alignment between the topup and eddy stages is preserved.
There’s also some changes on the way for the next MRtrix3 tag, that will simplify your use case slightly: dwipreproc will deal with this concatenation internally, rather than requiring that you do it beforehand. So in that case you’d just provide your single PA volume via the -se_epi option. Not sure at this stage how far away that change is from being merged to the master branch though.