The Hydrocortisone is a mild steroid to reduce the inflammation, and should only be used as often your GP prescribes.
The Aqueous is a light moisturiser and you can use it as often as you want but it's best to apply it no earlier than about 20 minutes after the hydrocortisone, as it can reduce the efficacy of the steroid. I leave it between half-an-hour to an hour.
Aqueous is very light and has even been known to irritate some skins. If it doesn't work there are plenty of alternatives. I found it fairly ineffective on my baby but Epaderm, which is much heavier and greasier, does seem to work.
It is a question of what suits your baby best. If the red patches don't heal in a few days it isn't under control, so don't hesitate to go back to the GP to ask for something else to be prescribed. It is best to get it under control now. Flare-ups are miserable for you and the baby.
I'm a bit amazed your GP was stumped. Childhood eczema is so common now they ought to know better. Mind you, we went through three GPs before finding one who really knew her stuff.
I found this book: "Eczema: The Treatments and Therapies That Really Work" by Dr Carolyn Charman and Sandra Lawton invaluable. It is aimed at the layman, very clear, and explains what is happening to an eczematous skin and the pros and cons of various treatments. It will help you get more out of your consultations with your GP. I got my copy from www.eczemaclothing.com
We top and tail rather than bathe most of the time (a shame, as he loves splashing about). Don't use soap or bubble bath. Try to dress the baby in soft, preferably cotton, clothing.
Oh, and washing powders and fabric softeners can cause irritation so you might want to change your washing routine. I can't recommend one brand as, unfortunately, what is fine with one person irritates another, but do make sure the baby's clothing is well rinsed. We have been through brand after brand and have settled on Magnoballs (hard water area), Ecoballs and Dryerballs for our baby's clothing. No powders, or softeners.
Good luck.