Well, if she is already on antibiotics, then the chances that she is panting as a result of some internal infection is relatively low.
Dogs pant for many reasons--hot, stressed, sick...no way to tell for sure. I think that having the vet look her over at this point will be the safest route and will give you peace of mind.
It's likely nothing major, but better safe than sorry.
As she the pups grow, eclampsia will be more of a risk when they are taking more and more milk from her. Talk with your vet while you are there about how to best supplement her and be sure to share with him any concerns you have regarding her diet at this point.
If hand feeding her for now is what you have to do to get some food in her belly, sobeit. Many new moms don't like to leave their pups for that long...even to eat or potty.
If she is eating, even small amounts several times per day, that is good. (Better than one larger meal, once per day, IMO.)
Keep us updated after you've had her checked and let us know what the verdict is.
