Mixing it up is good for the head. You're right though - running & cycling work different muscles - so the fitness gained in one sport won't translate necessarily into the other. From a logistics perspective - running is easier to do and sustain, especially with a busy schedule.
I tried to run in the morning and bike during the day - but waking up so early in the morning was starting to piss me off...
If you sit on your bum all day at work - I wouldn't be too concerned with overloading yourself. I'd play it by ear - if your legs are starting to get wobbly, take some time off. But if you can keep it up - why not?