As with any part of design work, the most challenging element is the creative aspect of the work: coming up with a design that's visually pleasing, colors, visual elements, etc.
But once you've got an idea you want to run with, here's how I used two fonts come up with the Umbraland logo in Adobe Photoshop CS:
I use a higher resolution and size to begin with and then, I can shink it down as need be. For example, the Umbraland logo is actually 15" or so wide at 300dpi.
I used one font (Augustus) to form the base of the logotype. From there, I began typing out random letters in the second font (Harrington). Conciviably, you could use as many fonts as you would like, but I advise sticking with a small number, or using very similar styles.
I look for interesting shapes that I may be able to use in place of or to augment the base font (such as the flourishes on the end letters of U & D, the middle connector of the M, the B and L flourishes, etc).
To "test drive" the looks of things, I throw on a layer mask to the second, stylistic font and then place it where I want.
If it looks good, I'll rasterize the letter and apply the layer mask.
For the sake of your sanity, I highly recommend grouping your work into different folders based on letters or sylables, as a particularly complex letter may have 4-5 different layers, depending on how you design it.
Once you have the rough design done, then go back and begin to smooth everything out. I'll make a copy of the pieces of letters (another reason to group everything together) and then merge it all into one layer.
From there, I'll adjust the tracking between the letters, adjust the bottoms and tops to make it all look uniform, and other touch ups.
So really, it's ultimately a matter or just experimenting to find what looks good.
I hope this is somewhat helpful - I've never written any sort of guide before...