There are many clues. Holmes determines the identity of Wilson's helper through his description:
“Small, stout-built, very quick in his ways, no hair on his face, though he's not short of thirty. Has a white splash of acid upon his forehead.”
and confirms it through his ears:
" Holmes sat up in his chair in considerable excitement. “I thought as much,” said he. “Have you ever observed that his ears are pierced for ear-rings?”
When he visits the shop, he calls Watson's attention to “The knees of his trousers" which are dirty.
The bank being directly nearby is another, and the time the master criminal gets Wilson away from work is a fifth. (There are others.)