AHCI is the newest controller used along with IDE & RAID. It provides support to the newer features on SSD's & Hard Drives, I.e. - Hot Swap drives. It is recommended to run SSD's in AHCI mode over IDE.
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?
I have 3 ssds, an intel ssd (38gb) that i use for windows and similar things, 2 ocz vertex 50 gbs and a 500gb 7200rpm hdd. which 2 ssds should i run off of which controller and which one should i run ahci off? Should I also not run my dvd drive off of ahci?
Since the drives are on different controllers, you set that controller to RAID versus AHCI. Also, remember TRIM is not supported by RAID, so you'll have to relay on "garbage collection" to clean the drive.