I'll keep this short and simple.
I suggest you grab a City Life map to help you in looking for these spots.
Chatham Road store
TST store (Shop 2112, Harbour City)
Tsing Yi store (Maritime Square)
For a complete list of stores and other information, click on this link.
If you ask me, Da Hood and Catalog are two of the best places to go to in Hong Kong for your sneaker needs. Both carry Nike SB and limited releases. Fa Yuen St. in Mong Kok is worth visiting if you've never been there but I find it a waste of time since 95% of the 30+ stores there carry the same stuff.
There are extensive Hong Kong Sneaker Guides but the stores I listed above will hopefully satisty the average sneakerhead.
More stores soon...