All of the P5Q series are based on the P45 chipset, the differences in models have more to do with secondary features like ports etc. It should not make any difference to you with using a quad core on either of these boards
The P5Q-E has:
1 x PS/2 Keyboard/Mouse combo port
1 x Optical + 1 x Coaxial S/PDIF Output port
1 x External SATA port
1 x IEEE1394a port
2 x LAN (RJ45) ports
6 x USB 2.0/1.1 port
8-channel Audio I/O ports
Accessories:
1 x UltraDMA 133/100/66 cable
1 x FDD cable
6 x Serial ATA cable
1 x 2-port Serial ATA power cable
1 x 2-port USB and 1-port 1394 (4-pin) module
1 x Q-Shield
1 x User's manual
The P5Q-Pro has:
1 x PS/2 Keyboard (Purple)
1 x PS/2 mouse port (Green)
1 x Coaxial S/PDIF Output
1 x IEEE1394a
1 x RJ45 port
6 x USB 2.0/1.1
8-channel Audio I/O
Accessories:
1 x UltraDMA 133/100/66 cable
1 x FDD cable
4 x Serial ATA cables
1 x 2-port Serial ATA power cable
1 x e SATA / 1394 bracket
3 in 1 Q-connector
ASUS Q-Shield