They do it based on average contract value, from what people can deduce (no official public formula).  For the 2007 draft, it broke down like this:

Last year, regardless of playing time or postseason honors, the third-round comp players had signed for at least $6.05 million per season, the fourth-round comp players had signed for $4.45 million to $5.3 million, the fifth-round comp players had signed for $3.5 million to $4.8 million, the sixth-round comp players had signed for $1.96 million to $2.6 million, and the seventh-round comp players had signed for $1.417 million or less per season.

JJ got $16 mil/4 years, or $4 million/year.  Reeves got a $20 mil/5 year deal, or $4 million/year.  Not sure what Nate Jones got, but Keith Davis got $3.5 mil/2 years.  

So, based on 2007 draft figures, we're looking at possibly two fifth rounders for JJ and Reeves, and two seventh rounders for Jones and Davis.  I bold the 2007 figures point because salaries have gone up since then, so the required money may go up even more and devalue the picks accordingly.

There are other factors involved, like what the player does for his new team.  If JJ or Reeves made the Pro Bowl or something, then we might get better compensatory picks for them.

And finally, I don't think resigning Flozell affects this; it's only for players we signed away from other teams.  So Zach Thomas might have some impact, but not Flo.

I'd love a 3rd rounder too, but I think it's more realistic for us to expect 5th round or less.