Unfortunately, I can only speak from experience (which is hypocritical because I always ask for "concrete" objective backing for answers from other people) and would love to see an answer with some solid backing.
I have been in the same sort of boat for a while now (coming up to 18 months with varying "job" component) and I can say with certainty that motivation is the key here. This raises a question whether your question should be changed to "How do I motivate myself?" from "How do I manage time/When do I do long hours?".
When you have motivation to put in long hours you put them in at any time possible. For example, when I had deadlines for my side-project I'd done normal 8 hours day on the job, grab a meal while walking down to the university where I'd do another 5-6 hours till midnight working on my own stuff either alone or with the team. I'd do at least 3 days like that. And then weekends.
When we met the deadline successfully and almost straight after the holidays hit such regime stopped because the motivation and adrenaline dropped.
So to cut to the chase:
- Re-evaluate your side-project. Are you serious about it? If yes, then why is motivation a problem? If not, then why bother?
- Make a plan with milestones which are broken down into achievable yet meaningful objectives. Only with a clear plan you'll be progressing and only by ticking things off the list you'll keep the motivation up.
- When you decided that it's serious and you are motivated, then make sure you don't burn out quickly. This means that while you can work 60 or 80 hours week, make sure you rest. Replace quantity with quality rest: sleep better, eat better, be active, get fresh air, relax in the true sense of the word. You need all energy replenishment you can get.
- Be productive. If you can be more productive then you can do the work which took 10 hours in 8, 6 or less. This site can help you with productivity techniques - just browse the highly voted questions, start with this one, for example.
I hope this helps.