1. Answer MAY depend on exactly what your BIOS's RAID utilities will do, but by far MOST do exactly that. The RAID system will put out a warning message when one disk fails. It will also put up a message about this during the POST sequence, so if you missed or dismissed the first message, there will be another every time you boot up - get in the habit of watching for it. The messages are important because the system will just keep things running from the good drive and you might not realize there is a problem if you don't look for the messages.
2. What you fear certainly can happen, and WILL happen if the new mobo's RAID system is made by a different company. BUT some chipset makers like nVidia and, I suspect, Intel, claim that their chips and RAID software will always use the same data coding system as new generations of hardware are developed so that a new future chipset made by the same supplier WILL be able to handle a RAID array created on an older chipset. Look for details of this on the websites of the mobo and of the chipset maker. I know I took advantage of this. I have a system for which I deliberately bought a mobo using an nVidia chipset because they promised this. A year later the mobo fried and I bought a new mobo with a newer but similar nVidia chipset and it just worked right away when connected up! I did not even have to do a Repair Install of RAID drivers - the new mobo just booted and ran from the RAID1 array I had in the original machine.
3. What OS are you installing, and where did you get the RAID driver? To install Win XP the driver will have to be on a floppy disk, but Vista and Win 7 can access other devices to install a driver from. It sounds like you have RAID drivers from two sources - one on the CD that came with your MSI mobo, and another from a different source (maybe the Intel website?). As an early step in the Windows Install process you will install ONE of these, but not both. I'd suggest the newest driver be used.
4. The Intel Matrix Storage Manager software is a very useful utility package for managing your array, so you ought to install it as instructed. I think that means installing it just like any other software package AFTER you have your OS installed and running.
On my machine the sequence was this: Install the 2 drive units along with all other hardware. Boot directly into BIOS Setup and configure the devices, including setting the SATA drives to the RAID mode. Set your machine to boot from its optical drive first, then the SATA drives after. Save and Exit and the machine reboots, but this time during the POST there's a prompt to hit a particular key combination to enter the RAID Setup utility. (Miss this and it will time out and proceed.) You hit the key and then within those screens you assign HDD units to a RAID array, then finish the array creation which basically takes care of the Partition and initial Format operations. (Note that, unless you specifically assign a HDD unit to a particular RAID array, by default it will be a NON-RAID unit.) When you're finished you make sure your Windows Install disk is in the optical drive and exit the RAID Setup to boot from the optical drive and start your OS Install. When that process asks you for additional drivers you install it (or them) as instructed. Once that is complete the Install process will be able to recognize that a Drive exists (happens to be your RAID array) available to install the OS on, and away you go. NOTE that the HDD's were first configured in BIOS, then assigned to a RAID array that is Created all BEFORE you start your OS Install Routine. Re-read you mobo manual to verify that this is the sequence for your particular setup.