You need to make sure you are taking vitamin d3 and not vitamin d2. (The huge 50,000iu weekly doses are often d2, and it is simply not absorbed into your body very well.) It also depend on how low your levels are. My levels were originally 28 and they tried to put me on that huge crappy dose of d2. I said I'd just supplement myself with d3, so I started taking 5,000iy daily. I wasn't always good about remembering, but I tried. Unfortunately, when my new doctor ran my levels again a couple years later, my levels had only risen to 36. That's just above deficiency level (depending on who you ask), but it is far from optimal. My doctor told me to take 10,000iu per day for th time being. That was last month, and coincidentally that is also the month I conceived after a year of trying. Vitamin d is important for so many function in our body, and scientists are only now becoming aware of what a wide range of functions those are.
I wouldn't stress over it. You've made it to 20 weeks already! However, I would definitely start taking a lot more d3 than you currently are. 1,000iu every other day (plus whatever little bit is in your prenatal) is hardly enough to maintain already optimal levels, and is nowhere near enough to bring up levels that are currently deficient.
Don't worry about it.
