what do you mean a different sata port? like 3gb of 6gb?
Typically, your motherboard will have two SATA controllers (native &/or JMicron/Marvell. The different ports (controllers) are represented by the different color SATA port. These have their own settings in the BIOS where you can run them in IDE, AHCI or RAID for example.
also i have a 500gb 7200rpm hdd that i store files on. is it alright to run off ahci?
Yes, it is okay to run the drive off AHCI.