How can I manage the time of my research project under uncertainty?
Unfortunately, this sort of uncertainty is just part and parcel of the life of a researcher. I've been doing research for 15 years now, I run my own research group and this is still a problem for me. 


With this in mind, my first piece of advice is not to feel alone in this. The uncertainty is not because of your inexperience. We never know how long research will take because, by definition, we don't know the answer yet, thats what makes it research. 
Keep a notebook (real or computational) for each project/idea category and write your thoughts in them. 
Celebrate any concrete progress however small.