Hello Kale and welcome to the guild. You have come to the right place as there are loads of people here who can help you with general mapping and many who can help you with MapTools. Then there is me who is the dev of ViewingDale and I am very willing to help you out in all things about that app.
First of all ill point you at the fabled tut on viewingdale here at the guild. Fabled, cos it took me an eternity to get around to writing it. If you look on the menus under Quick Links is now (thanks to RobA) the keyword index which is also linked on my sig. Under ViewingDale you will see some links relevant to the app from the guilds post history.
Ok, now on to your question. What scale to use. Well ViewingDales job is to display maps at any scale. I call it scale independent. So if were talking about scales like 1:50000 or 1:1000000 or whatever then your fine, its easy. The main point is that you enter the size of the map in as real units. So lets say you have a bitmap (BMP / JPG / PNG) of 2000 pixels by 1500 pixels and the scale on the map shows a bar 400 pixels across with intervals on it that show that the 400 pixel bar is 100 miles. Ok your map is 2000 * 100 / 400 in miles => i.e. its 500 miles west/east and presumably 1500 * 100 / 400 miles => 375 miles north/south.
When you import an image in you can hit F2 for "Images and Icons" and then "Convert (Import) image". You hit the "Load Colour picture" button and find your image. Then you would do the same if it had a mask on the transparency but for a map this is unlikely. Then "Save final Image" and place it somewhere that is sensible. So create a new folder for the world that your using - like Middle_Earth, or Toril or whatever - and then go into that folder and put in the map image by naming it and letting the system save it.
Now you must create an icon for the image using the "Create New Icon from Image Wizard". You hit each button in turn. So set its name with "Icon Name". Use the "In Directory" to set the directory or create a new directory for the icon with your world name and use that. Then the next button you find the image you just created. Then in "Width" put in "500 miles" and in "Height" put in "375 miles". On a map I would click the button for "Default Origin" so that its in the corner and then hit the "Create it" button.
Your map should appear as the main icon now.
Say your map was really big tho and was 6000 x 4000 pixels. In that case I would use the included app which is in the main directory for the program called "ViewingDaleImageSplitter.exe" with the icon of 4 little boxes. If you dont have this app then you need to update to the latest version (1.08 at time of writing) and it will be there. See website about "version control".
What this app does is do the same process as described above but all on one process and it will split the image into more manageable tiles at the same time creating directories of the tile images and icons. You can pick the tile size but 512 or 1024 is a good starting bet.
Once the app has finished then load the new icon with the L key or F2 images and icons menu again and find it where you told it to be. I.e. in "Worlds/Ansium/".
In either case you should find that the scale bar at the top of the program will show it at the correct real world scale. If you have calibrated your monitor (see tut or help file) and the map was of large scale like a battle map then you can zoom in to 1:1 scale and the screen icons ought to be exactly real size on the monitor.
Anyway, the idea is to make everything in real world size regardless of the pixel dimensions of the images used to make it up.
When exporting for map tool then you need to set the scale to something like 100 pixels per 5 ft. ViewingDale makes this pretty simple. Use F4 or the "System Settings" and then the "Save Main View as picture file". Where it says "Set pixels (dots) per inch" hit the button and enter 100. Where it says scale put in 60 (Thats 1 inch picture = 60 inches real world or 5ft - i.e. standard fantasy scale) and then it will find for you the image width and height which if not large scale might be too big to be sensible. Now if someone from MapTools can say that they can import a map of non 1 inch to 5 ft scale then say so. Anyway thats the usual battle map scale image for MapTools I believe.
Though it might be said that it is not an easy app to use (at least to start with) and I think thats somewhat justifiable, I think it has the best capability for mapping a whole world at once and I think its probably fair to say that MapTool has the best playing features and its certainly the most popular playing format where the map and miniature movement is concerned so the two together is a good choice I think.