To make sue of those free IRQ's you have to turn off the devices before you install the OS. In some cases, you may have to manually assign the freed IRQ's to the PCI bus in the BIOS.
The COM ports are the two serial ports, and the LPT port is the printer port. All ATX class motherboards I have ever seen have these devices on them and the BIOS should allow you to disable them.
I do not need the LPT port as my printer is a network printer, and the COM/serial ports are a waste of motherboard space these days, unless you use one for an external modem, but you can still disable the other one that is not being used.