Patterns are always opaque, but you can "flatten" them into pattern 0/1 (transparent white/black) by using "Edit -> Invert" twice on a selection.
Depending on what you're doing, you may also need to turn on "Style -> Transparency", which controls whether selection movement/pasting treats the selection as transparent or opaque.
The other feature to be aware of when working with transparency is "Style -> Transparency Mask", which displays transparent pixels as a mid-tone gray to distinguish it from opaque white. With Transparency Mask mode on, the white color in the palette is opaque white, instead of transparent white.
