(Disclaimer: I'm not a PCR expert, but...)
Did the two housekeeping genes generally agree with each other? That's the important thing. There are papers on how to evaluate this. I'm not expert on that, so I won't give much advice, but in some cases housekeeping gene selection is important because a good control gene for one experiment, may have variable expression in another case (with different tissues, or cell activations, and etc.)
Also, the reason for using housekeeping genes is that using a constant RNA input concentration in the RNA cannot always control the experiment enough. For example, if genomic DNA is present, the DNA will be quantified along with the RNA regardless of how many times it is repeated. Other contaminants can also be present.
I use a different formula, but I think that if you think it through, or test it on samples, you'll find that it doesn't matter if the experimental Ct is larger or smaller than the housekeeping.