So, this is more a Nipype question than FMRIPREP, per se; I have no experience using the SGE plugin (or any plugins apart from Linear and MultiProc), but I would expect the parallelism to be at the Node level. That looks like reasonable YAML, but I'd try loading it to make sure it generates the right Python dictionary to be sure.
When we run FMRIPREP on clusters, we tend to use
MultiProc and submit jobs on a per-subject basis.
As far as specifying the amount of memory per-job, it's really going to vary widely, but I assume there's some reasonable default (e.g. 1GB + 1 CPU per Node). This may be a situation where we need to systematically add memory estimates to the metadata of many nodes before SLURM or SGE plugins can allocate resources efficiently. (Again, I don't really know, here.)
Hopefully someone else can give a more helpful for using Nipype with SGE. (@mgxd perhaps?)