Do I need to bid on the item in ebay as well, or just on ibidder?

Short answer: you don't need to bid on eBay when you set up your snipe.

Long answer: the sniper places your bid on eBay on last seconds. If you place your bid manually on eBay, the sniper will make no difference.
The only exception when you want to bid manually first is when you want to make sure your seller has no restrictions set and your bid is allowed. In this case you just place a minimum manual bid, not your full amount.