How little that which thou deniest me is; (line 2)
For an unmarried woman in the seventeenth century sex was a big deal. The speaker's goal throughout the poem is to make this big deal seem as tiny as a flea.
It suck'd me first, and now sucks thee, And in this flea our two bloods mingled be. (lines 3-4)
The mixing of the two bloods inside the flea is seen as being equal to the sex act. We also get the feeling that the speaker is trying to turn the woman on with this image.
Yet this enjoys before it woo, And pamper'd swells with one blood made of two; And this, alas ! is more than we would do. (lines 7-9)
Like a child stamping his feet, the speaker is like, "But the flea gets to taste your flesh without having to woo you! Not fair!" The poem itself is the act of wooing. Also, notice that he never speaks directly about sex, as if that might scare her off. Instead, he uses vague language like doing "more."
Where we almost, yea, more than married are. (line 11)
They are "almost" married because their bloods have mixed, but they haven't had, you know, like the whole ceremony, without which you can't be married! Jeez. On the other hand, they are "more than married" because they have already consummated the marriage inside the flea.
Just so much honour, when thou yield'st to me, (line 26)
Not if, but when. You can say one thing about this guy: he's got confidence.