If you are curious as to why the controller has the functionality to swap the turntable side, it is due to the original Beatmania having both 1P and 2P turntables on the right side.
Presumably, when Konami was developing IIDX, they realised that not only does it look better to have a symmetrical cabinet design with the turntables on the outside, but is does make more sense for right handed people to play with the turntable on the left and cover the keys with the dominant hand.
You might notice that there are a lot of Japanese players who will play with the TT on the right, simply because they started playing Beatmania and naturally used the player 2 side when they progressed to IIDX.
I fit in to this category too as I also started out on the original Beatmania and went through a patch where I thought I was restricting myself by playing on the right despite being right-handed. The answer is that there was no reason why my left hand should be weaker so I stayed where I was comfortable and made an effort to increase strength and dexterity.
I also found that playing with the turntable on the right is like typing on a keyboard (for me at least). I use my left little finger to hit the shift key or the first white key in IIDX. My right thumb hits the space bar or the last white key in IIDX and my right pinky jumps out to hit enter or hit the TT in IIDX so it feels like a similar setup!
I guess what I want to say is that once you find a comfortable position, you should probably try and stay relatively close to that position while you are getting better. Once things heat up a little, you will find that just three fingers from each hand is not enough so you will automatically start bringing in your thumbs and little fingers, these are definintely recommended! Good Luck man!