You can do either.
or you can do both.
You can a power commander and have the bike dyno tuned to suit the modifications you have done to your bike to maximise power etc.
You can also buy a flashing kit and do that FTECU, Woolich, Brentune are commonly known options.
You can also remove your ECU and send it away to several different providers (moore mafia is one recognized one I know of) who will flash your ECU and send it back to you, then you just plug it in and ride.
I had a 2008R1 for close to 10 years. I first put a full exhaust system on it, and deleted the 02 sensors, and AIS and did a few other things.
I initially out a power commander5 on the bike and ride it like that for a while.
A couple of years later I decided to go with a flashing Kit and I went with FTECU. My reasons at the time were that I wanted to remove the ignition and go keyless (I lived outside the US at the time, and the country I lived in, the '08 Non - US model came with a coded key and an immobilizer, and the FTECU software allowed me to remove this, among other things.
One benefit the FTECU had was that I was able to directly import PC5 Maps into the ECU, so I downloaded my previously custom tuned map and uploaded it into my first flash, then sold the power commander.
You can also take the bike to a local shop that uses whatever flash provider you have purchased and have them tune it for you without ever needing a power commander.
Before you go into this rabbit hole though, it helps to knw what xactly you are working with and what exactly you want to acheive?
Is your bike stock right now?
if not what mods are on it?
if it IS stock, what mods are you planning to do? exhaust? air filter? purely cosmetic stuff?
f you can answer this, we can better advse you on your best course of action
