Depending on how many staff are on duty and whether or not there are other customers, you may be ushered to a specific seat. The bartender may also ask you to take any seat you like. You also may be asked if they can take your jacket and/or umbrella.
It's important to note here that cocktail bars in Japan are structured more like restaurants, i.e. the staff considers the bar full if all the seats are taken. There may or may not be space to stand, but either way, everyone must have a seat. The concept of a seat doesn't go away just because there isn't a physical seat -- even standing bars may be considered full when the standing seats are full.
I’m Whiskey Richard, and I am the founder of nomunication.jp. I’ve lived in Tokyo for over a decade, and I am a certified Shochu Kikisake-shi/Shochu Sommelier (焼酎唎酒師), Cocktail Professor (カクテル検定１級), and I hold Whisky Kentei Level 3 (ウイスキー検定３級). Click here for more details about me and this site. Kampai!