I have some problem with your "small basil plant", but you also say that it has large leaves.
What I do:
I cut the flowers, so basil will continue to grow the leaves and new branches. When I do it, I cut down with few leaves (I keep the leaves for me). By doing this, the basil will create new branches blow the cut, so with season (and Sun) I get more leaves. Sometime I cut some branches, not to have dense basil (and usually when I need many leaves).
The beginning of season is more tricky.I buy basil when they have just few leaves. Usually I wait when basil seems healthy and it is growing. In such case I may take some leaves (maybe cutting the top branch) on one plant (note: I have few plants, so hopefully one can growth better, for next time I need basil). Possibly this is your case with "small basil". Just before taking leaves next time, I would wait that basil will have more leaves then last time.
I never use the large leaves (the bottom ones), always the top one. And I tend to cut them late afternoon or evening (ev. before midday). It is about the use: to have fresh leaves. I do not think it matter for the basil.