Z Offset - hardware calibrated vs slicer - simplify3D  

Z Offset - hardware calibrated vs slicer - simplify3D

Hi guys - I am new to Prusa, but not 3D printing. I have been using a Lulzbot Min and Cura Lulzbot edition for about 1 year now. (Recently, I was having hardware problems with my Lulzbot - and found out that Aleph Objects laid off all their staff and sold all its assets to FARGO and is no longer supporting its customers at the moment - which is shame.) - I wanted to get another printer that had great reviews and found Prusa. I am very excited however to now own a Prusa, but I know I need to relearn a little bit. 

I purchased an already assembled i3 - after turning it on and watching it go through its steps - I realized I did not cut the cable ties underneath the bed. After doing so - I feared I might have screwed something up - so ran a full reset calibration. I performed a LIVE Z offset and was able to get the filament to look like the one in the handbook and it adhered well. I printed the whistle from the SD card and it looked great - though there was a bunch of loose filament inside the whistle - I assumed that was normal - but is it?

NOW - I wanted to try one of my .STL files via USB using Simplify3D and a i3 profile I got from a friend. I tried to print a small joystick button - and it appeared that the Z axis was too high. The filament did not look squished and the button crumbled.

My question - can a Prusa profile used in  simplify3d or other slicing tools override the tool head Z axis settings / offset? I assumed that since I adjusted the setting on the hardware it would respect that height. I assume I am missing something.

What I have seen so far is  that this is an amazing printer - I wish I would have just got one of these first instead of dealing with the lulzbot headaches.

Thanks for your time.