Planning milestones and time

Question

I was hired by a marketing company a year ago initially for link building / SEO stuff, but I'm actually a Web developer and took the job just in desperation to have one (I'm still quite young and just finished 2nd year of University). From the 3rd day my boss realised that I'm not into that stuff at all and since he had an idea of a web based app we started to plan it.

I estimated that it shouldn't take me longer than two months to do it, but as I was making it we soon realised that we want to add more and more stuff to make it even better.

So the development on my own lasted for about 4 months, but then it became an enterprise size app and we hired another programmer to work along me. The guy was awesome at what he did, but because I was assigned to be programmer/project manager I had to set up milestones with deadlines and we missed most of them, because most of the time it was too much work, and my lack of experience kept me setting really optimistic deadlines. We still kept adding features and had changed the architecture of the application twice.

My boss is a great guy and he gets that when we add features it expands the time frame in which things should be done so he wasn't angry at me nor the other guy. But I was feeling bad (I still am) that I suck at planning.

I gained loads of experience from the programming side, but I still lack the management/planning skills which make me go nuts. So over the last year I have dedicated probably about 8 months of work to this app (obviously my studies affected it) and we're launching as a closed beta this month. So my question is how do I get better at planning/managing a project, how do you estimate the times? What do you take into consideration when setting goals.

I'm working alone again because the other guy moved from the city. But I'm sure we'll be hiring to help me maintain it so I need to get better at it.

Any hints, points or anything on the topic are appreciated.