How do I get 200.6% map completion?

Here are the completed maps. There are 1890 rooms in total. Unfortunately, the only way is to carefully comb over them to find the discrepancy.

There is a slight chance you can find the missing room by purchasing the Castle Map from the Librarian. This map will reveal a set portion of the non-inverted castle in a darker shade of blue to indicate unexplored rooms. However, it is highly likely that these rooms have already been visited as it is only a small percentage.

In addition to the maps provided in the accepted answer from user9983, I'd like to add a few bits of information, as well as a tip, all of which I hope helps players out in getting a full 200.6% map completion.

First off, the two castles are comprised of the following number of rooms:

Normal: 942 rooms (100%)
Inverted: 948 rooms (100.6%)
Total: 1890 rooms (200.6%)

You can fully explore the normal castle before going to the inverted castle. Technically. Sorta-kinda. Bear with me for a minute, here.

Once you defeat Richter in the normal castle, the game is programmed to automatically take Alucard to the inverted castle. Upon arriving, DO NOT go anywhere, but check your stats. You should be at 942 rooms - meaning you completed the normal castle*.

Technically. Sorta-kinda.

Because the game takes over, and forces you into the inverted castle, you "missed" one room in the normal castle, and got one room in the inverted castle - thus, your being at 942 rooms. Immediately transport back to the normal castle, and jump/Leap-Stone/Bat/Mist/Gravity-Boot yourself directly upwards to claim the room just above the teleporter to the inverted castle.

Check your stats one more time, and voilà! You should have 943 rooms - that is, 942 (a full, 100% normal castle) + 1 (inverted castle).

Using this method, you can know whether you've fully explored the normal castle or not, before beginning on the inverted castle.

*If you have less than 942 rooms, you missed something.