This is not very complicated. Each drive is mechanically mounted in your machine and has two connectors to it - one power, and one data. Since you want to use the 750 GB unit for Windows and boot from it most often, connect its data cable to the mobo SATA_0 port, and the other one to the SATA_1 port. There is no such thing as Master or Slave in a SATA system, so no settings or jumpers need attention on the drives. If you also have a SATA-connection optical drive, plug it into another SATA port. If it is connected, instead, to an IDE port by itself, make sure it is set as the IDE channel's Master.
In your BIOS Setup screens (usually enter by holding down the "Del" key when you boot up), ensure the screen that controls the SATA ports has them Enabled. Likewise, if you have devices on the IDE port(s), make sure they are Enabled. Go to the first Setup screen that gives details of the drives attached and just check that the BIOS can see them all on the right ports.
This next setting depends on your choices and what OS you are planning to install. If you will be using Win XP or earlier, there's a problem that it does not know how to use SATA devices without installing drivers from a floppy drive during the first installation process. To get around that, BIOS's often have an option to make the SATA device pretend it is an older IDE (aka PATA) device. If you need this, go back to where the SATA ports are set up and look for an item that talks about what mode to use - IDE (or PATA) Emulation, native SATA, AHCI, or RAID. Unless you need RAID, stay away from it. The IDE (or PATA) Emulation mode is the one that makes your real SATA device appear to Win XP as a plain IDE device.
BUT if you are installing VISTA or Win 7, this Emulation really is not needed. Those more recent Windows already have all the drivers needed for SATA or AHCI modes built in, and in that case you should set your BIOS to one of those modes. Read up on what AHCI does for you versus native SATA - there are small differences which may not be any advantage to you, so native SATA would be better. As far as the relationship between SATA modes and Linux - I know nothing. My guess is Linux should be able to handle native SATA.
Last adjustment in the BIOS is to set which device(s) to boot from. When you get there you should have all of your devices available to choose. Usually it's not one device, but a priority sequence. For example, in my machine I set this: 1st choice is my floppy drive; 2nd choice is the DVD drive; 3rd choice is my main hard drive; fourth choice is none. People with no floppy will not put that in, obviously. Some BIOS's will let you choose in one of these positions a USB drive that is set up to act as a bootable hard drive. When set up this way, a machine trying to boot up will go through the sequence looking for a bootable device; if it fails to find one, it skips down to the next automatically, and only fails if it finds nothing bootable anywhere in its list. It boots from the first one it does find and stops looking.
This is one way you can easily set up two OS's on two drives. In your case you make the 750 GB drive on the SATA_0 port a bootable device and install Windows on it. Then you make the 350 GB unit on SATA_1 also a bootable device and install your Linux distribution on it. Initially you set up your Boot Priority to use the SATA_0 drive, even if it is in 3rd position after a USB drive and the DVD drive. But any time you want, you can reboot into BIOS Setup, change that to booting from the other SATA drive on port 1, save and finish booting. It will use the Linux boot disk from now on until you change it back again.
Once you have these set up this way, here's how I suggest you install OS's. Disconnect the 350 GB drive on SATA_1, set the BIOS to boot from SATA_0 AFTER the DVD drive in the sequence, put the Windows Install disk in the DVD drive and boot up. Tell it to install to the (only) SATA drive you have and complete it all. When done, shut down, disconnect the 750 GB unit on the SATA_0 port and reconnect the 350 GB on SATA_1, change the BIOS to boot from that port, and put your Linux Install disk in the DVD drive. Install Linux to the (only) SATA drive you have now.
When done, reconnect both SATA drives and boot once into Linux so it can recognize that a new drive (the 750) has been added. Reboot and go into the BIOS to set it to boot from the 750 GB on SATA_0, save and finish the boot into Windows. It may now recognize the addition of that 350 GB unit. I say "may" because I honestly don't know if Windows can deal with a drive Partitioned and Formatted by Linux.