I got the concepts of distant supervision. As for my understanding, the creating training data process is like;
I got confused at this step. What if there is more than 1 relation between these two entities (e1 and e2) ? If so which relation should I select?
It depends on the model you're training.
Are you learning a model for one kind of relationship and doing bootstrapping? Then only pay attention to that one relationship and drop the others from your DB.
Are you trying to learn a bunch of relationships? Then use the presence or absence of each as a feature in your model. This is how Universals Schemas work.
Here's an image of a feature matrix from the Universal Schema paper: