To mark the characters, just type their initial in the cells. Sometimes you'll need to use a smaller font and put two initials to identify a character - players rarely coordinate to make sure everybody's name starts with a different letter. I usually use numbers for the monsters. You need to use a different number for every unique monster. In games that have a one-hit-minion rule (M&M, 7th Sea, 4E D&D, etc), you can use the same number for each mook. Once again, you may need to reduce the font and use two digits, but only if you are a cruel GM intent on slaughtering the party. You can put a legend on the side to identify everybody.
Once you have the map done, you need to put it into the portal. When you have the map on your screen, take a screen shot of it. In Windows, this is Alt+PrtScrn. For a Mac, it's Command-Control-Shift-3. Then paste it into your favorite image editor and crop it appropriately. I suggest keeping the row and column identifiers in the picture so that people can address specific squares, such as H7. If you don't have an image editor that can crop pictures, I suggest IrfanView (http://www.irfanview.com/). It's free and easy to use. (I don't have a suggestion for a Mac program, but there are lots of image editors for Macs). I suggest saving the file as a GIF file. GIF will usually make a smaller file for a simple image like this.
Once you have the file, simply go to Map Builder and create the map.
The first trick with using drawing tools is to learn how to snap things to the grid. This will help you place things exactly. It can be turned on and off as needed. First, make sure the drawing toolbar is showing. Right clicking on any toolbar should give you a list to make this visible. Go to the draw menu on the toolbar and choose snap and to grid on the submenu. This will not save with the file, you'll need to turn it on the next time you open your document.
The first change we'll make is to make counters for your characters and monsters. This make changes a little easier than entering text into the cells. You can drag the counters around as they move. It also lets you make larger creatures. Draw a text box that is one square high and one square wide. List the initial in it. Make sure to click out of it instead of hitting enter. Hitting enter puts another line on the text box, which makes your text disappear. You can adjust the font to make it fit well within the box. You can also change the shading and border of the text box to make monsters and characters look different.
After this, we can make our environment more interesting. Borders make good walls, but they can only do straight lines along cell edges. You can use the line tool to make lines at any angle. Just click it and draw your line. If it's not the same width as your borders, you can right click it and change the properties. Under autoshapes there are other tools that can make arcs or other shapes. The scribble tool under the autoshape menu lets you draw rough cave walls. What's more you can right click on the scribble and choose edit points to make fine changes to your cave.
The next trick is to make common symbols like stairs and doors. These items usually have details that are smaller than grid scale. Most people would turn off snap to grid and try to draw them by hand. This makes things all sloppy and messy. A better answer is to scale it up when you create the symbol. Take the standard gaming map symbol to stairs - a series of lines getting progressively shorter to the down end. Draw the lines using snap to grid taking as much room as you need. Then select all of the lines, go to the draw menu and choose group. This makes this whole collection one object. It can them be resized, copied and modified. The green dot allows you to rotate the symbol so you can use the same symbol in different orientations. If you can't quite get it rotated to the right angle, right click and format it. One of the tabs lets you select the specific degree to rotate it to.
Doors are another object that works well with groups. They are narrow rectangles that sit along a wall line. While stairs ususally fit in suqares, this one doesn't match up well. The solution is to make the door part of a bigger object. Use the rectangle tool to draw a box eight squares long and one square high. Select the box and choose properties. Set it to no fill and no line. This makes an invisible box. Remember where you put it! When you move your cursor over it, it will turn to the resize cursor when you're over the edge of it. In the center of it, draw a box two squares wide by one high. Group these two objects, and resize them to two squares wide by one tall. Now you have a door.
Sometimes you'll want to hide part of a room. This is easy to do with drawing objects. The triangle is a good one for this. Draw a line from the character with the best sightline past the object. Then draw the appropriate shape and delete your guide line. Sometimes this shape will cover the other objects, and sometimes they'll float over it. Excel has tools to control which objects are on top. Right click on the object and select "Bring to front". This will make sure your fog is on top of anything else.
But what if you want hexes? The simple answer is to offend a witch. But if you are talking maps, I have two suggestions. The first is to use the hexagon autoshape to draw one four squares high and four across. There's a yellow handle to adjust how wide the outer edges are. Set it so that the top and bottom faces are two squares wide. It's not quite a regular hexagon, but it's close and it tiles well. The other way to do it is to use offset squares. Make a 2x2 square, then make another one down one row. This is topologially equal to a hexagon, but more compact. When you have as many hexagons (of either type) as you want, select them all and group them. Because the entire area is a picture, you'll sometimes have trouble selecting the background.
Practice with these techniques and combine them and you can do some amazing things.