Perhaps it's a silly question but I've recently purchased a new motherboard and of course it came with a CD with it's drivers only for Windows systems (you know, the Autorun cr@p and all that)
So, should I somehow try to obtain these drivers from the vendor for my Linux system or is that not necessary since the OS installation will take care of it by itself?
In the Linux world (this isn't specific to Ubuntu), drivers are normally included in the operating system. Anyone writing a new driver is encouraged to contribute their work to the Linux driver, and that usually happens. Each new release of Ubuntu comes with more supported hardware. So, ideally, you should not need anything besides what Ubuntu provides.
However, if the motherboard model is recent, there might not be drivers for all of its features yet. Usually, the manufacturer takes care to have Windows drivers ready the day the product ships, and the Linux development only starts when a developer receives a board. Some manufacturers collaborate with Linux developers. The best among them follow normal channels and have their drivers incorporated quickly in the official kernel and in distributions (this is more common on server equipment, less on desktops and laptops). Other manufacturers provide token Linux drivers — rushed, low-quality, hard-to-install. Yet others do nothing.
What you should do is try installing the latest release of Ubuntu and see if it works. It is rare for manufacturer drivers to hold an advantage over official Linux drivers when the official drivers exist. If it doesn't, do a web search on your motherboard model and “Ubuntu” to see if others have solved the problem for you. If you can identify the component that doesn't work (e.g. the disk controller, the sound chipset, …), do a web search with that.
If it doesn't work and your search doesn't turn up anything, ask here! Be sure to give as much information as possible: the exact motherboard model (with a link to the description on the manufacturer's site so people can easily find out what components it includes), a precise description of what happened (black screen, disk churning for a while, beeps, error messages, …). If there are any error messages, transcribe them exactly (if you're in a situation where you can't copy-paste, a legible screen photo is better than nothing).