how do I get it to recognise a CD-ROM drive.
This should already be configured. Which version of AF do you have ? You only have to change something if you have more than two CD drives.
how do I costomize it and be able to save it that way so that the next time i use it will load up the way i left it
First you have to install it to HDD. You cannot write to the original CD. Then you have to choose the "save" option of whichever program you use. All changes in AmgaOS are temporary until you save them. To save an icon position choose "snapshot" from the menu.
Bye,
Thomas