Bike training on stationary bike?

I have a crazy work schedule, where I'm up and out the door by 5:30, at work from 7 to 4, and home around 6.  I suppose I could go for a bike ride when I get home, but I really dislike riding at rush hour/dusk.

So, because I get here so early, I joined the gym across the street.  2-3 times a week, I've been spending 40 minutes on the stationary bike.  I limit my time to 40 minutes because that's about all I can afford to be away from my desk in the morning.  I go back at lunch to do weights. (I get to work 7 hours days and call it a "full day."

So... what should I be doing in that 40 minutes?  For the first couple of weeks after starting this schedule, I would set it on level 7 "hills" and just go.  Then, last week I decided to do a "manual" workout and make up my own intervals (usually 3 minutes hard/1 minute recovery).

On the weekends, I aim for a longer, REAL bike ride OUTSIDE with real wind and real hills and a real bike. 

My question: is this a good plan?  Is there anything in particular I can do to make it better?

TIA