If you have a mouse on Com1, do not use Com3 for the modem. Com1 normally shares the same IRQ as Com3. Com2 shares an IRQ with Com4. Of course, you only have 15 IRQ's in total and most will be needed for other devices. Most modems have jumpers or switches to set the Com port, Plug and Play modems will also have a PnP setting that will let Windows assign the port and hex address.
Some modems are software configurable.
If your mouse is not on Com1, use Com3 or Com4. If your mouse is on Com1, use Com4. Most modems come already set to Com4 as a default. Choosing either a PCI modem or an ISA modem has no effect on modem speed, either slot is more than fast enough for a modem. As with any add in card, once you open the computer case you will need to select the slot you will use.