i think you could upgrade at first and second however. To do that I think at least one of your third basemen on your bench is expendible along with cordero, maybe you can use them and your current 1bman and 2ndbasemen to upgrade.
from what i can see, you have a "decent" team...upton has HUGE upside (i picked him up)...your pitchers should do ok for you...not really sure how your scoring is...so i don't really know what to tell you...sorry
Strengths: Pitching (both relief and starting), right side of IF, bench
Weaknesses: OF, left side of IF, speed
Your OF isn't bad, but it's not your biggest asset either. Ideally, I think you want Delmon or Rios as your third OF, but you're using them as 2/3. Lee is a fairly good #1, but it would be great if you could add a more legit #2 (maybe Delmon or Rios can be that, but I'm not 100% convinced). I'm thinking someone like Abreu or Wells.
Jeter and Atkins are great. I'm not convinced by Upton just yet, but I guess he brings some speed to your team. Fielder might be ready to take the next step and join the Konerko/Delgado tier, but it might be another year or two away. I do like his potential though.
Obviously your closers are great. You potentially have 3 top 10 RPs.
Your starters are scary good. Santana, Sheets, and Halladay? Are you kidding me? That's about as good a 1-2-3 punch as you can get. Burnett and Bush are a nice back-end of the rotation and although Zito's not my favourite, he doesn't need to be a stud for you. Still, you might want to see what kind of trade value he has in your league if he can string together a couple of good starts.
Your offense lacks a true masher, which is likely the result of you passing on big bats early in favour of Johan. I think you have enough quality bats though in Atkins, Jeter, and Lee that your offense should still be competitive. Ideally, you'd add another power bat (hopefully in the OF) by swinging a deal for some of your strong bench guys. I'm thinking something along the lines of Rolen and Delmon Young for Vernon Wells and a decent back-end SP? Just a thought.
1B and 2B are your weakest positions. you have a lot of SP's...do you have GS or IP limits? if so...having that many starting pitchers might be a terrible waste of bench space. Upton has upside that i really like...so what i'd try to do is package a SP and a 1B for a better 1B...or maybe a 2B in case upton doesn't pan out the way i think he will...