No. The Linux partition is your PS2-Linux root partition. It is required to run Linux. The swap partition is required to properly deal with the very low real memory in the PS2 (32MB of which you can use about 30MB). The FAT partition may be deleted after installation if you have moved the important kernelloader elf, kernel, and initrd to the memory card and reconfigured kernelloader to start from there. I don't recommend deleting it until you are sure you understand how PS2-Linux is booting, and that it does not need these files on the FAT partition.
also one of the partitions in the linux usb image will be used for linux, its ok if i delete that right? all i need is the fat and swap partitions right?