Question : Problem: Two Hard Drives . And I don't know how to set them up .

 I'm running windows 98 se . A Duron prosesor . On a MSI mobo . And 512 RAM .  I have a 40 gig Western Digital HD . And just installed a 80 gig WD-HD . I did all that I was supposed to do with the new drive . That turned out just fine . Then I loaded windows 98 se on it . I can jump from on drive to the other . I did lose my desk top . I'm figuring I did something wrong . Some of my programs wont load . What I want to do is back up all that I can . With my CD burner . and just wipe all of it clean . (both drives) And just start over . But I need to know the best way to set it up . Simplicity is what I'm looking for . I like win 98se . So I'll stay with that . I new at all of this , and still learning . I just need something I can print out and use while I'm starting all over .  Thanks ahead of time !!!

Answer : Problem: Two Hard Drives . And I don't know how to set them up .

What I think is that u must reinstall ur both the drives.
Go through the following steps as i explained below:--

1.First backup ur necessary data from both the drives on cd's with cd burner

2.Than make the 80GB as ur primary HDD and 40GD as slave by either changing their IDE connection or through jumper setiings. (here making 80GB as primary will increase ur system performance)

(Note:-- Please after changing HDD connections make sure that both drives are shown in BIOS.)

3.Than Boot the system with another bootup disk or startup disk

4.After booting go throug FDISK for both the drives. Create new partitions according to your need.

5.After FDISK reboot system and format all the partitions.

6.After that just install win98se on dirve c: and other progrmas that are necessary for u.

7.Than just backup ur files from the CD' to ur system
 
Please dont try to install same windows i.e.,win98se  on both drives. if u wish u may install some other windows on other drive so that u can work on multiple operating systems and enjoy the features of both windows.

Thats it

I think this will help u
if u are not cleared about anything than just ask here