I think it's good to add in extra calories right now. Your body is not efficient yet at doing these other exercises. I'm sure you felt the need to eat more when you first started doing 3hr bike rides regularly. It's going to take your body a while to adapt to your current routine, and you might want to take more rest days. At least every few weeks (maybe once every month or two?), take several days off one week and focus on recovering. Get a massage. Stretch. But only do light activity. Then resume your normal schedule the next week.

The hard thing about doing triathlon is that it's nearly impossible to really excel at every aspect. Every person who does it tends to have a strong background in one of the sports (more commonly, running or swimming). The thing is to try to capitalize on your strengths and to minimize your weaknesses on the others. But the way your body needs to work, something that helps in one (say, extra upper body muscle for swimming) can tend to hurt another (cycling).

If you start to really struggle everywhere, if you feel run-down and/or wired at night, or if your HR data is not what you're used to, then you are probably overtraining and need some serious rest.