This overrides the one on your computer. External modems are limited my the computer's UART, though. Making an internal modem work can be a real nightmare because of IRQ and COM Port conflicts. Your modem cannot share an IRQ or a COM port with another device. To change your modem settings, you'll need your manual.
Most modems come configured for a certain setting.
If this doesn't work and causes conflicts, you'll need to change it. Again, consult the manual for the jumper configurations. Other modems have DIP switches. During installation, you will be asked to select what type of modem you have from a list. Try to pick the exact modem.