Attenuators are just a resistive circuit. It generally is considered something you should avoid, but you may not realistically have an option. Basically anything you run your signal through will color the sound to some extent. Using attenuators are no different, but you may not really be able to discern any difference at all, so you don't need to avoid them at all costs.
As to where to run the V3, this notion you should run it analog out so you are just hitting the first amber lights drives me nuts. It is just a rule of thumb someone came up with for their particular gear, and now everyone seems to spread it around like gospel (no offense gratefulphish, just wanted to set the record straight). The first amber light really has nothing to do with anything in the grand scheme of things.
The V3 will absolutely, positively not overload on the analog outputs if run above the first amber -- it'll be fine all the way up to clipping (but not at the clip point). That is, the V3 in and of itself is perfectly fine being run very hot on the analog outputs. I run mine all the time with it going all the way up to >-1db (all three amber lights) going analog in to my 722 -- no problem at all.
The issue isn't the V3 overloading on its analog outputs, the problem is overloading the analog inputs of the downstream gear. And the V3 puts out a very hot signal -- +25dbu max. My 722 can take +25dbu, so it is no issue running the V3 as hot as I'd like. If your gear takes a lower maximum input before overloading (brickwalling), then you need to reduce the output of the V3, simple as that.
For instance, my MT can only take a +3.8dbu signal at a maximum. The V3 puts out +4dbu when just the first 2 green LEDs are lit. So if I even hit the second green LED on the V3 going analog out to the MT, I will overload my MT. The first amber light people talk about so much correlates to an output of +16dbu on the V3's analog outputs. So with just hitting the first amber on my V3, I will overload the crap out of my MT.
For your specific case of the MR-1, Korg lists the maximum input level as +6dbV. +6dbV is the same as about +8dbu, so the max the MR-1 is +8dbu. The V3 puts out +10dbu when the third green LED is lit, so you'd need to run the V3 so you light up no more than the first 2 green LEDs. If you hit the third green LED, you're overloading your MR-1, with even worse overloading if you hit the 4th green LED. If you hit that first amber LED on the V3, you'll again (like the case of the MT) be overloading the crap out of your MR-1.
I really don't see running your V3 so low that you really can't see what's going on with the meters, so I'd really suggest getting a pair of attenuators. -20db attenuators should do it.
[I will say that what I've said about the V3 and MR-1 is based on published specs, not trying things. But I can say for sure that you can run the V3 much hotter than the first amber without any problem when running into the 722. And the first amber is way too hot for running the V3 into the MT.]
Sorry for the long-winded post, but I'd really like to totally get rid of this notion that running the V3 at the first amber LED is the right place to be running it when running analog out.