Trust your instincts, T.!!!! You are right on the money. This sounds exactly like our son. You are astute to suspect the formula as it is very, very likely to be the formula - cow's milk based and soy based formulas contain the TOP TWO most allergic substances for infants (dairy and soy!).
It could be that he's reacting to any/all dairy or soy he's getting (whether via formula only or by both formula and your breastmilk, esp if you had antibiotics during or after his birth which affects the lining of your stomach). But to truly test, your *best* bet is to take him off the formula for at least 7 days to see if his eczema improves (24 hours won't tell you much - you'd need at least 5-7 days). Here's an excellent article on feeding sensitivities in babies - this talks about breastfeeding but absolutely applies to formula feeding as well:
http://www.kellymom.com/babyconcerns/food-sensitivity.html
http://www.wondertime.go.com/learning/article/interview-c...
Also, if you're worried about not "topping him off" with formula for a week... make sure you put him to the breast as he shows you his hunger (aka not on a schedule you impose) and your supply should increase to meet his needs. Thus far, when you are giving your son formula to "top him off" this only makes sure that your supply won't keep up with his demand --> your body will make as much milk as your son tells it to make. If you feed him a bottle, your body doesn't know that your son is eating and to make more food for him.
Again, if you decided to remove the formula for a week to test whether this is the cause of his eczema, remember to put him to the breast whenever you see early signs of hunger so that your body will get the signal and will increase your supply to keep up with his demand (which will be A LOT at this young age, birth to 12 weeks is a HUGE time of growth and therefore very, very frequent breastfeeding).
I see that you're returning to work soon - is your work allow its employees smoke breaks? If so, they should allow you breaks to pump breastmilk for your baby. You'll save a lot of money by continuing to nurse, and even more if your son is allergic to dairy/soy (very common in infants these days!) as the hypoallergenic formulas are ridiculously expensive. A nice, double electric breastpump (like a Medela Pump-in-Style or an Ameda Purely Yours) runs from $200-350 brand new and *will* save you HUNDREDS of dollars in formula costs (formula over time will cost *much* more than $300!!!).
Even if you are not interested in pumping while at work, you can absolutely breastfeed while at home and this will still save you $$$. While some babies transition to formula without any problems, many babies DO have problems and just really, truly need their mothers' breastmilk (don't do as well on any substitute).
I wish you much determination in doing this detective work to find the SOURCE of your son's eczema - no cream will cure it, only removing the irritant (whether it's the formula or pet hair from the family cat) will truly resolve his discomfort. Best of luck! Having been there myself with my own son, I can only say it is *very* worth it. I eliminated all dairy and soy from my diet when my son was 5 weeks old because his face was full of angry, red, dry, scaly eczema (via my breastmilk, and I was shocked - didn't have this with my 1st!). Within 7 days of my being dairy free, my son was a new person, comfortable, slept well, clear skin, no eczema. It was so gratifying to see the change and that was extremely motivating for me in terms of changing my diet (removing all dairy and soy). We were off of dairy for over 14 months, only recently reintroducing it into my diet and my (now toddler) son's diet to see if he'd outgrown his allergy/sensitivity. Just trust your gut... mother's intuition is so powerful!!!