I deal with possible muscle atrophy a lot, and risk of muscle loss. Though I've never tracked it carefully, here's what I know anecdotally.

One, staying active is key. This has sometimes meant doing simple bodyweight exercises when I'm otherwise in a place where I would be sedentary. I've actually found that bodyweight / isometrics are more effective than weight training, at least in terms of feeling leaner and stronger.

Two, I try to eat more protein earlier in the day when moving, and more carbs or fat at night to both help with sleep and with muscle maintenance while I'm resting. I've found that doing this keeps my muscles fueled and I'm able to bounce back more quickly, thus able to stay active and keep building muscle.

Eat protein. Have a cup of cottage cheese before going to bed. Have whey post workout.

to avoid muscle loss durring weight loss two things are needed. eat more protein. use your muscles.

Apart from increasing protein, possibly have a look at supplementing with BCAA.

I personally take just short of 10g (a level tablespoon of powder) in the morning, and then the same pre-workout. I lose muscle really quick too and am currently playing with a http://leangains.com IF schedule. I make sure I am not reducing calories at all but simply fulfilling my calorific goals in two meals. I certainly feel pretty good, I have started tracking my weight and development this month. But as they say you can simply use a mirror or judge by how your clothes fit. Sounds stupid but I watch how well my GAP stretch tshirts fit.

I have found that ectomorphs are usually under some sort of metabolic stress or a hormonal flux of some sort. My primary thoughts are that histamine or cortisol could be high. This is why the 'eat more protein' etc doesn't always work.

For myself it was histamine was the culprit, when I stopped sneezing; muscle loss stopped being an issue when having extended training breaks.

Probably look at why you have atrophy, maybe look into HGC?

First thing I'd do is go visit your doc and get a complete hormonal and thyroid panel. Being generally lean but struggling with belly fat seems to me a possible body composition issue that seems caused by a bad hormonal profile. So checking for total and free testosterone, DHEA and estradiol may give some insight. If low testosterone, then maybe that should be what you should address, and I bet you'd instantly see some improvements in muscle mass. If not, then let's look for other reasons.

Thyroid issues may also be playing a role. When not working correctly they make energy balance and body composition a difficult thing. So full test of TSH, free T3, T4 and reverse T3 could show us some things going on.

If you can check for HDL and LDL ratios and HS CRP It would give an idea on overall body inflammation state, if there's an issue with inflammation then you can bet I'll manifest in difficulties on metabolic function also that can halt your progress.

Also a salivary cortisol test may be useful. If you were under sever stress then all the rest of the hormones would be downregulated and you would enter catabolic state which is muscle breaking. You want to be in an anabolic state, that is an optimal body state to promote muscle growth or at least maintainance mode for what you have gained in the past. Also don't underestimate your need for sleep.

Having plenty of protein and proper training as recommended on the other posts is needed and an important part of the equation, but for the whole picture, a correct hormonal balance is also needed and equally important if not even more.