My custom tools are –
Layouts: Has big rough (soft) pencils and thick markers on it.

Pencils: Has my refining pencils, some markers and buttons for new perspective Ruler, parallel line ruler, etc..

Inks: has my inking tools. If you haven’t been go to http://www.frenden.com and search his blogposts for Manga Studio. There’s one that’s has his settings for brushes. Best. Settings. Ever.

btw, are your inking layers set to Black and White (two bit) or Greyscale ? I’ve found that b&w is the best setting for a layer that I’m going to throw down inks on.

In the palette itself, I have multiple copies of the same pen, the only changes are the size of the “nib” and I go from Small (left side) to Large (right side). That small –>large arrangement is used for Pencils and Erasers.

Then there’s the Color set, which has the burn and dodge tool and the blenders.

On my Intous 3 tablet, I’ve set the right side Express buttons, next to the touch strip, so the default Shift button is now a pen size larger shortcut and the default Opt button is now the pen size smaller shortcut. I think that the keyboard shortcuts are open bracket and close bracket — don’t recall if I set the keyboard shortcuts myself or if it’s a MS default.