There's a lot of conflicting material on this matter.
The older Epic
background (Adeptus Titanicus
, Space Marine
1st ed.) had the Imperialis (the winged skull) as the symbol adopted by the Imperial Guard after the Heresy. I believe this was in honour of the Loyalist faction's campaign army badge*; but I'll stop short of stating that as a fact, as my memstacks are hazy!
Prior to that, the Emperor's forces (which presumably include the Imperial Army) used the thunder and lightning device that was the Emperor's personal sigil (this is the one present on the Mark 1 Thunder Armour models). The Eagle (n.b. not Aquila) was a common device, but not specifically related to any one person or insitution.
Meanwhile, the Aquila (i.e. two-headed eagle) in Rogue Trader
was the symbol of the Imperium; with the various parts representing various bits of the Imperium. I have vague recollections that there's also a contemporary source that has the Aquila representing the two Empires – the Imperium of Man and the Martian Mechanicum. Can anyone validate that?
The newer material has the Aquila as the Emperor's sigil, and little distinction is made between the single and two-headed versions – which I think is where a lot of the confusion about who can use it etc.
Personally, I think it's a bit weird when it's implied that the Astartes couldn't use the Aquila, while everyone and everything else – including ammunition crates – seemingly could. It'd make more sense to me if the Eagle (or similar device, such as the Thunder-and-Lightning device) was a common image, while the Aquila was reserved.
I'd suggest that you use either the Thunder-and-Lightning device or a single-headed Eagle device; and have the Aquila as restricted to heroes or noteworthy individuals (exactly as for the Astartes).
Alternatively, since the Army is very much a reserve force in M31, you could rationalise it as less uniform; and not have a single unifying device at all. That way, you can go mad with cool symbols like Lions' heads (the M41 Imperial Guard are increasingly symbolised with lions in the most recent material), or a symbol of your own choice.
That said, I think it'd would be best, aesthetically speaking, to have something distinct. Winged devices (such as the Eagle, the Aquila and the Imperialis) are very common to the Astartes and M41 Imperial forces. Since Imperial Army models will have no recognisable visual equivalent to the Pre-Heresy armour marks of the Astartes, if you want to have them as recognisably Pre-Heresy, you'll be rewarded by working more creatively than simply rationalising existing symbols on the models you'll use as the basis.
Imperial Army will require work to make distinctively Pre-Heresy. There's no simply answer for their symbol, so take advantage of that to make up something aesthetically distinctive.
*Adopted by the Loyalists (everyone – Astartes, Mechanicum, Army) to distinguish themselves from the Renegades, who were still using the Thunder-and-Lightning symbol... which, amusingly enough, had eight-points and was pretty much the Chaos Star!