When you want to dive deeper, Manga Studio certainly lets you. Features are in place to add the distinct screens and tones that give manga its look many artists and readers are enamored with. Again it's nothing you can't do in Photoshop (especially for those of us well versed in its use), but I'm trying to give this program a decent run through.
The screen system takes a little getting used to, tho it comes down to dropping screens from a library into a selection you make. Sadly many of the advanced tonal features are restricted to the EX version, but the Debut version does allow a fairly full library of screens to be added. The cool thing here is that screens can also be applied to the pen tool, allowing you to ink right in the tone's pattern.
The layering system allows for masking, which makes adding in background elements alot easier and adjustable. Manga Studio has a Speed Line filter, and I have to admit this is very cool. It's so cool the filter control dialog is in freaking Japanese Kanji. Not sure why they didn't localize this, I'd prefer it in English, but it's not hard to figure out thru playing with sliders. Here I've generated some speed lines I'd have balked at attempting on paper: