I also have trouble losing or even maintaining weight while I am cycling frequently.  I know I unconsciously justify overeating because I need to "fuel my ride."  
I have recently started a food journal with calorie count based on Nancy Clark's "The Cyclists Food Guide."  I don't believe she would be very supportive of low carb diets, but would encourage healthy whole grains and fruits, just not empty carbs.  She gives you a formula for figuring a rough estimate of the base calories you need for daily living (which you can also easily find online on many different websites) and then a formula to figure what additional calories you need for riding based on your weight and average speed and time in the saddle.  If you want to lose weight at a healthy pace and maintain your metabolism and energy level, you then decrease those calories by 20%.
I'm not counting carbs or anything other than calories because I just don't like to do that.  Calories are about all I can handle.  I have cut out refined flour and am eating more lean protein and whole grains.  No junk.  
It has been very helpful to me to have a guideline for how much extra I need to eat on riding days.  For example, a 140 lb person cycling at 13mph for 2 hours needs an additional 980 calories.  If you are trying to lose weight, reduce that by 20% and add an additional 784 calories to your base 
amount that day.  I have just started doing this so can't report results yet, but it has to be better than what I have been doing!  This Friday will be my official weekly weigh in, and the first since I have done some riding, so we'll see then.
				
			 
			
		 
			
				
			
			
				
Grits
2010 Trek 5.2 Madone WSD, SI Diva Gel Flow
2002 Terry Classic, Terry Liberator