If pd*14>archery than will it count in damage in different way?
If by archery you mean archery wpf, then yes.
If you have less wpf (remember: armour reduces wpf too) than what your PD needs, then you will only get the PD bonuses of whatever level of PD you got the WPF for.
Example:
If you got 10 PD you would need 140 wpf to not get any penalty.
If you only have 130 wpf, then you will only have PD 9 (since 14*9=126) so you'll only get the bonus damage and missile speed
* that PD 9 gives you and not the PD 10 that you have on your character.
If you only got 120 wpf, then you will only have an effective PD 8 and so on.
Also note that the wpf you need for each lvl of PD actually
removes that much wpf from your character, so getting more PD may or may not reduce your accuracy. See footmark for why.
*Possibly an extra accuracy bonus too, but cRPG might have removed that and/or that's why the wpf penalty for PD negates.