I honestly couldn't imagine playing Wizardry 6 without mapping it. There aren't very many things on the screen that would help navigate; all the features of a room are described in text. When it says there's a desk and chairs in a room I kind of have to take its word on that. So yes, without a map you will probably be pretty lost.
If you're using this program where to start drawing is really a non-issue. You have unlimited map space so it's not like you'll be running into the edge of the page anytime soon. North is towards the top and in Wizardry 6 you'll have a spell to tell you which way north is. I don't recall a compass in Might and Magic but for that game I assumed the direction I faced upon exiting the inn was north. Also helpful is that M&M I's maps are 16x16.
In Wizardry 6 you can see nine tiles at any given time any further and it's just darkness. You'll see the tile you're standing on the two tiles to the sides of you and six tiles, 3x2, in front of you. Eventually you'll learn to spot the difference between a wall that's right in front of you and the walls which are 1 or 2 tiles in front of you. So when I map I find the tile that I'm standing on, use the compass to find the direction I'm facing and draw two squares in that direction and any other squares I feel confident in drawing.
The program has lines to represent walls and, more importantly, doors. If you see a door, map it, save (always save), check to see if it's open and then change it if need be. I find it's easy to use the number keys at the top to switch the door drawing from a closed one to a locked one. "1" is an open door "2" is a locked one. I changed the color of the door to differentiate a gate from a plain door, especially since the "knock-knock" spell doesn't work on gates.
Stairs belong on their own tile and should be drawn directly above or below the stairs on the following floor. This will help keep the floors directly above one another which will help in various scenarios. After a while your map will begin to take shape and you'll be able to see what the castle looks like architecturally, pretty cool.
The map progress will help you identify where you've yet to go so if you get stuck it's fairly easy to peruse the map carefully and see which doors or gates have yet to be tested with a particular key. Screw-ups are inevitable so don't feel too bad if you have to go back and correct something. I've made at least 2 screw-ups so far. As long as you keep casting "Direction" you should keep them to a minimum.
I can't think of much else to help you map that isn't blatantly obvious. Note what the room is (King's bedroom, Storage room, etc.), note the effects of fountains, locations of buttons. Use colored lines or tiles to represent hazards.
Yeah I don't know, just some things I've found useful. If you have any other questions feel free to ask.
edit: Also, I drew the first floor of Sorpigal (M&M) by hand, it was surprisingly fun but slowed the game down to a crawl. This program only made grid-based mapping about a thousand times easier to do.