On average most button top batteries are 1mm longer than the flat top counterpart, with the SMPL mod this may cause the button to protrude past the outer bottom edge of the mod depending on how close it already is. I own two SMPL mods and strictly only use Flat top batteries in them with absolutely no problems, you simply need to ensure that the positive portion of the atomizer 510 protrudes at least 1mm from the end of the threaded(negative) section.
Do you know specifically which batteries you purchased? the 35A rating is a burst drain specification used by a few different makers now, there are no commercially available cells that exceed 30A CDR so I'm lead to believe the battery you purchased is most likely a re-wrapped LG HE2, which IS available as a button top and will work for your application, provided it doesn't cause an issue with the button as I spoke about above. Keep in mind most of what I said regarding what battery it may be is pure speculation, without pictures or a link I have really no idea what battery it is.
Even if the battery you purchased does turn out to be an LG HE2 it's still a 20A CDR rating which is well above the ~11A your build is using, well within a safe threshold and a good battery.