First of all how long is the event you are training for? If the bike leg is not the ironman distance and a more normal distance then endurance is not something you need to worry about. Your 1 hour trainer session should be more quality based and since you are doing running intervals the 30-40 mins 2nd bike ride should be recovery based, or just putting in some miles.

I would leave the long endurance rides for the weekend when you have the time and then it is important to ride it in its entirity. ie. you need to ride the full 3 hours not split it into 1.5hrs in morning and afternoon. Its important to teach the body to be able to handle the longer rides and during longer rides on the bike the body is learning to adapt to this.

hope that helps
anne