OED2 lists it under catawampous, which dates from 1840. Google Books shows seven examples of that spelling in the 1840s, then no more. It was replaced by "catawampus", first recorded in 1843. Judging from Google Books, "cattywampus" originates as a pronunciation guide for "catawampus" in 1901, but isn't used in its own right until the 1930s. Since then it's slowly been gaining ground on "catawampus", but hasn't caught it yet.
I think of this word as having a similar connotation to "wabi sabi," a phrase/concept which i read about long ago in Utne, which means "the beauty of imperfection." Life is asymmetrical, out of alignment, askew, f'd up, etc. I find a certain comfort in appreciating that state of affairs.