Hi Gozde,
Thank you for your email.
The choice of regTemplates and flipTemplates is up to you. Some people generate an average of the whole population after running the whole SPHARM-PDM pipeline once, some other people just randomly choose a single mesh of the population representative of the anatomy to be the regTemplate/flipTemplate.
For the flipTemplate is worth mentioning that the new SPHARM-PDM extension now incorporates a module to do the flip of the parameterizations easily. Also, see the new documentation here.
There is thread here in which we discussed (among other things) how to create average meshes in SlicerSALT-SPHARM.
I hope this helps.
Best,
Bea