/vr/ - Retro Games

The other Dojo(the one with Sekishusei, the old dude) lets a character get bonuses for the waza they learn, such as better attack or accuracy, but stat drops accordingly, higher attack usually lowers accuracy or increases SP cost.
The Varque(I don't know the exact romanization of that) lets you see your profile and input passwords for campaigns.
The center castle lets you organize you party members and formations.
The Storage(left from the center castle) holds excess items or items you get from bonuses/campaign check it out if you see a ! mark on it.

The Magic Research Center and Blacksmih can be upgraded by sacrificing characters, maxed characters fill double the amount of bar uncapped characters can so always use maxed characters or low tier ones on those.
Sacrificing characters in other buildings gives you marks to use in the shop.

Last but not least, once you start a quest you'll see three icons on the bottom, those are stage items that have different effects, the left one(Flower Charm) increases stat growth, the center one(Imperial banner) lets you use a VERY strong attack on a quest boss, the right one( the stone heads thingies, I don't know the kanji for the first part but the last one stands for Doll)prevents one LP loss per stage.
Do not use them lightly as they're only acquired through Level/Login bonuses or if you're fool enoug to give money to her, through Kabakko, Kabakko(pic related) is a kid in a hyppo suit( a joke character derived from a RomaSaGa 2 monster) that will give you random items if you give her money, she can be found randomly during missions.