If you have an internal, jumpered modem, you must configure your card to either COM3 or COM4. In the Devices preferences panel, pull down File | New Jumpered Device. Set the Device Type to „Serial Controller,“ and set the IRQ 4. Under I/O Port Ranges, select New and enter 0x03e8 (for COM3), length 8. When you press Done, you’ll see: 0x03e8 – 0x03ef.
The address for COM4 is 0x02e8 – 0x02ef, IRQ 3.
If everything went well, you now can use the Modem Settings control in the DUN panel to choose the right COM port for your modem.
Good Luck!

The following information was once the tip „Add jumpered device on COM2,“ but has been consolidated into this tip. This information comes from Isen Kusima (cycnus at geocities dot com).
If you’ve got a modem wired to COM2 but the PPP panel only shows you options for COM3 and COM4, here’s what you do:
1. Open the Devices preferences panel.
2. Go to New Jumpered Device | Modem.
3. Choose COM4.
Now, if you watch Devices carefuly, you’ll see your modem.
4. Double click on the modem (in the Jumpered Devices section).
5. If you choose COM4, you don’t need to change the IRQ. (COM4 and COM2 use
IRQ 3… if not yet IRQ 3, change it to 3).
6. In IO Port Range: change 0x02e8 - 0x02ef to 0x02f8 -
0x02ff.
7. Reboot.
If you reboot and get an error message saying your video card isn’t supported, return to the Devices panel and look at the Resource Usage tab. Check to see if there are any conflicts listed there. If there are, you can fix them manually. Alternatively, you can go enter your machine’s BIOS (usualy by pressing DEL or F2 during boot and search for „PCI and PNP Setup.“ Make sure you set „IRQ 3 used by ISA“ to YES so that no devices other than your modem will use IRQ 3.
Remember:
COM2 & COM4 use IRQ 3
COM1 & COM3 use IRQ 4
If the user want to use COM2, the easiest way is from COM4. The user only needs to change the resource (change the ‚e‘ to ‚f‘, 2e8-2ff — in other words, 2f8-2ff). The IRQ is already set to IRQ3, since COM2, and COM4 share the same IRQ.
Same for COM1 — set it up from COM3, change the ‚e‘ to ‚f‘, 3e8-3ef — 3f8-3ff. The IRQ is already set to IRQ4, since COM1 and COM3 share the same IRQ.