Print settings in PrusaSlicer vs in-Printer? Also trouble with NinjaFlex.  

Print settings in PrusaSlicer vs in-Printer? Also trouble with NinjaFlex.

Newb here, learning how to print. I'm sure this question has probably been asked but I'm not even sure how to search for it.

I am trying to print NinjaFlex and having trouble. I made the mistake of trying to manually customize all the print settings in PrusaSlicer for the model I tried printing. I used recommended settings from somewhere on the internet - I do not recall exactly where. I did make sure to set all of the various print speeds to between 10-20 mm/s, 240º/50º. Then I exported the g-code, popped it into my i3 Mk3s (Firmware 3.8.1) and tried to print. 

The printer head began zipping at speeds that had to be much faster than 10-15mm/s  since the filament was barely oozing out, unable to make it to the plate. I went into Menu > Tune > Speed (I don't recall if that is exactly how it was worded, but something close to that) and saw one setting labeled "Print Speed". It was set to "100" even though I exported the g-code with all the various settings below 15-20mm/s. I turned the Print Speed down to "10" and it definitely slowed the Extruder down.

Why didn't my settings in Prusaslicer (and presumably the g-code) transfer over to the printing (the printing by default was way too fast)? I haven't tried the basic Semiflex or Flexfill profile in PrusaSlicer yet, so maybe I missed a setting? If I did miss a setting and print speeds/etc. are supposed to carry over, how do the settings under Tune relate to the printing? 

Another issue was, even after slowing the print speed down to 10 under "...Tune", there still seemed to be a lot of under extrusion happening. I saw another setting called "Flow" and tried turning this progressively up to 500 but it didn't seem to make a difference. 

Can anyone offer advice? I'm going to try the default Flexfill profile next.