And in this flea our two bloods mingled be. (line 4)
Although it sometimes seems that the speaker is all over the place, this poem actually proceeds in a very logical fashion. He sets up the idea of two bloodlines mixing, symbolizing marriage, within the first four lines.
O stay, three lives in one flea spare, Where we almost, yea, more than married are. (line 10-11)
The second stanza is directly focused on the idea of marriage. Using that single small word, "yea," as a bridge, the speaker makes the giant leap from "almost" to "more than." From this point on, he no longer even worries about trying to establish that a marriage has taken place; it's a given.
This flea is you and I, and this Our marriage bed, and marriage temple is. (line 12-13)
Maybe it's not the best idea to compare your marriage to a blood-sucking parasite...or to say that both the wedding and the honeymoon have taken place inside a bug.