1. When I try to save my configuration to floppy it appears to have been saved. However if I click on the floppy icon on the desktop it says the file is not available. Any help with this is appricated.
try typing sync in a console (dos prompt), did you mount the floppy first? mounting/unmounting is one diference in Linux. mounting means making it acessible to read, write... unmounting "disconects" it...

2. I have an intel based computer with a pci modem. The modem was not found and configured. I did not notice this at first because I was connected the first test on a highspeed through lan.
I decided to connect my external serial modem and it was found just fine. Can anyone tell me why my other moder was not found?
some modems are so called winmodems, that is they only have drivers for Windows, and those drivers are used to "simulate" a real modem in the operating system. yours sounds like it is one of those. not impossible but hard to get working in linux, defenetly a hard experience for a beginner.

3. Last thing may seem simple but I am just confirming this. I am only testing this on a test computer the first day not my regular machine. I do believe from everything I have read that the program does not touch my hard drive in any manner. I ask because I can read the hard drive and see the contents. Just want to make sure everything is run from ram.
it only reads no writigng unless YOU alow it.