I did my twin training on the 220T Seneca III and when I first started I thought I'd never be able to get the hang of the throttles.
The problem is the wastegate is fixed, so at full throttle at sea level you are pushing too much exhaust gas through the turbo, and subsequently overboosting the engine. The higher you go, the less dense the air and the more you can open the throttle. For the model I flew you couldn't fully open the throttle below FL110 without causing the lights to come on and full power at sea level was about half way open.
Baring in mind how little in the way of engine instrumentation you get in a Seneca, its probably a fair assumption that when the orange lights do come on bad things will eventually happen to your engines. Also, a point worth considering is that during my training I was told that I could illuminate the overboost lights twice during my CPL for a short period (ie, go around or stall recovery), so long as it wasn't much above 40 inches, without failing, any more than that and it would be a partial. So, even if it doesn't trash your engines its not a good way to pass a flying test!
What I found was that after about 10 hours of flying I developed the necessary muscle memory to be able to consistently set 40 inches most times. It just comes with practise - in the go around, whack the levers up to where your arm knows 40 inches is then leave it and wait for the turbo to kick in. Don't be tempted to readjust the throttles too quickly, the turbo lag always takes longer than you think, and if it felt right when you set it, it probably is.
The preferred method for stall recoveries was set the throttle for about 40 inches, bring the flap up, sort out the pitch, roll, etc, then go back and readjust the throttle if the MAP was either less than 39 or the orange light was on. It was understood that the power was difficult to set and you had more important things to do at the time, so a certain leeway was granted, the important thing being that you set about the right power.
Anyhow, enjoy the Seneca, one day you will line up on the runway, ram the throttles up and exactly 40 inches will appear on both sides, on that day you will feel like a king!