Hi;
the central connectors are used only to "close" the circuit when battery holder is used. There is no connection with both central connectors and internal circuitry.
If you hold the calculator in it's "normal" position, say, NOT upside down, and face its back side, the leftmost battery connector is the negative (and the rightmost is the positive) for a 6Vcc power supply. You should use batteries, no AC adapter of any kind; these connectors are DIRECTLY connected to all internal digital IC's, including LCD controller. When I want to read magnetic cards or use the wand (barcode reader) I use four N-size, series connection. I have read at least 300 sides (about 150 cards; I do not have so many cards, I read and write in the same pack). That's one of the most current-consuming operation. The HP41 alone will use a few milliamps to operate, no need for huge current amount.
If your calculator has two golden-plated contacts in the button face of the square hole you mentioned, it's a bit more easy to connect a power supply (still batteries). Keeping the calculator in the same position, I use the topmost (LCD as a reference) as negative, and the other as positive. That's the actual place I connect the external batteries assy, and when I do it, I remove the original battery holder.
Hope this info will help you. If you need something more, post again.
Success.