(Just wanna toss my two cents in.) I just finished a manga for the final project of my Bachelor's Degree, and the biggest thing I can suggest is: GET MANGA STUDIO! Especially if you want to do the traditional screentoning style.
I tried for years to find manual screentones that you lay over your artwork and found out they no longer sell them anywhere outside of Japan, and they're incredibly expensive. Next, I tried using Photoshop to mimic the effects of screentones, but ran into difficulties with moire patterns and it was just so much hassle. Also, putting the book itself together in InDesign was difficult.
With a tablet and Manga Studio, I was able to complete projects quickly and well, and the learning curve was easy with the help of the site
Pencilkiller.com (Holy cow, I sound like a Manga Studio salesperson...
eek ) Get the real version, not the demo. If you're a student, you can get it half-off if you delve into their website.
Aaanyway- I personally do most of the work manually before transferring it into Manga Studio. I'm lazy, but I find that a regular mechanical pencil and computer paper works just fine for designing and drawing. I recommend Micron pens for inking. (Sharpies for the large black areas.) If you can wield a brush well, Higgins ink is relatively cheap and works fine, but don't paint over it with watercolor.
Design the pages in small thumbnails, about 2 inches, in the correct format. I suggest drawing them actual size so you know if it's too busy, but always ink at at least 150%, 200's better.
Good luck, and I hope this was helpful. Please don't repeat the mistakes I made!!
If you wanna see my work,
My Deviantart and
My Website