ATMega328P-PU and 328P-AU im planing to make my very own arduino design based on the Arduino PRO mini. I picked this board instead of the UNO mostly because it's way more simpler compared with the UNO since the USB-to-Serial part is missing. As many of you know the MINI uses the 328P-AU which is the SMD version of the 328P however since the AU version is too small for me i would like to use the PU (UNO's chip) instead. From the datasheets the only difference is a small change in the pins position. And the one million dollar question is: Is there any difference on those 2 chips? If i try to use the same design just with the PU model is it gonna work?
The -AU and -PU suffixes on the part name indicate different packages. The former is used for the "32A" package (32-lead TQFP), and the latter is used for the "28P3" package (28-lead DIP). In plain English, the -AU is a surface-mount part, and the -PU is a breadboard-friendly chip.

As far as functionality, there is virtually no difference. The 32A package exposes pins for ADC6 and ADC7, which are not available on the 28P3 package, but they are otherwise identical. (Note that these pins are only used for the ADCs; they are not a member of any port, and thus cannot be used for digital I/O.)