+1 what Bill said
Also, call or email Emagair and talk to Brad or Trent. Their customer support is fantastic. Service and support after the sale is amazing. Don?t miss the opportunity to get their advice.
Page 13 of the manual says to install the mags in a convenient orientation. You mount according to your needs. I can tell you that ANY choice you make will have pluses and minuses because of limited access. I also suggest you take pictures of a mag from all angles so you can remember where different parts are and also read the labels on the case. Once the mags are installed they are tough to access and/or see...as you already know.
Remember you have to be able to see the LED to time them so plan for that as well. I have the IO-390 and it looks like a 2 person job to get them timed.