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Every account shares the same Inbox mailfolder for receiving messages. You can change the default behaviour in the account preferences dialog under the Special Folders Tab. This enables you to use different mailfolders for each account and makes using multiple accounts more convenient.
When using File->Get New Messages for, you can choose which account you want to check. Selecting File->Get New Messages item (or by pressing Ctrl-T) makes it easy to check for new messages in all accounts simultaneously.
The composer lets you choose the outgoing mailserver. When replying to messages, Columba automatically tries to guess the correct account for you. You can choose one account to be your default account. This is the account Columba chooses when it cannot determine the correct account and it is also the default account when opening a new composer window.