P&D says "These sessions are done after a thorough warm-up and often towards the end of a general aerobic run or recovery run. Allow yourself plenty of time between repetitions so that you can run each each one with good technique... A typical rest is to jog and walk 100 to 200 metres between repetitions."
Personally I run them so they're all done in time for a 1 mile-ish cool down, 100m on, 100m(ish) off (just linearly as part of my usual out and back runs, no backtracking or messing around on a track).
I've done it three times (I think, maybe 4), it's fine, what bad things have you heard about it? The loos were a bit grim last year but that's true for most races, the support is good for most of the course, the route doesn't really take in Edinburgh but is pretty enough. The organisation itself seems pretty good, the pens at the start work well, I've never had a problem with water/tshirts/medals/etc. The only area I recall hearing people complain about is the coaches back at the end, I have never got one so can't really comment on that.
It's a great race, have fun! I got the train back last year, I think I was stood up but it wasn't crowded like a commuter train over here, there was plenty of space to move. I'm sure I could have got a seat if I'd tried.