How a connection is chosen

The four checks BooleanSMTP runs, in order, to pick which connection sends an outgoing email, down to PHP mail as the last resort.

BooleanSMTP checks four things, in order, until one of them names a connection to send through.

A connection the sending code asked for. Some sends name a connection directly — a resend from Email Logs, for example, reuses the connection the original message went out on. That connection is used without any further check.
The connection that owns the From address. Every connection can have its own From address (see One connection per sender); if the message’s From address belongs to one, that connection sends it.
Your Default Connection — or your primary connection. Set Default Connection, under Settings → Delivery & Reliability, to be explicit about which connection handles everything else. Left on System Default (PHP Mail), BooleanSMTP uses your primary connection instead — your most recently activated active connection, if you have one.
PHP mail — WordPress’s own way of sending mail — when none of the above found a connection at all.

Next steps