When you created the disk you would have used a screen similar to the attached image. There should have been a message upon completion indicating the disks were completed successfully. You should also be able to put the disks in another computer (not meaning to run them but just to look at the data) and see that there are files / folders on the disks.
Two ways to use the disks -
1)Most eMachines are supposed to open the recovery utility when you press the F-11 key repeatedly while booting (saw that some will do the same with the R key) Once in the utility there should be a menu with choices for recovery. This should recover the system from the hidden recovery partition or . . . it may ask for you to insert the recovery disk 1 if it does not find the partition.
2) Boot to the recovery disks and get the recovery screen for the utility. Again there should be a menu for recovery options.
Both are independent of Windows and should run regardless of the existing Windows install with a fresh install of Windows being done at completion.
It is difficult to give a walkthru on a system I am not familiar with but usually it a straight forward menu that guides you. My concern is that your recovery disks were not created successfully or that . . . when you try booting to disk 1 . . . your system is not booting to the disk but rather to the hard drive as it usually does. If you have set the DVD drive as the primary boot drive and the booted recovery disk does not recover the system then, again, I would say the disks were not completed successfully.
If the disk creation failed, most manufacturers sell the recovery disks for individual computers on their web site for a nominal fee (usually $25 - $30)
I only use the manufacturers recovery as a last resort which seems to be where you are now. Might try to reboot, pressing F-8, and use the last good config option or get into safe mode. If you can get to Windows, try making the disks again, should not be allowed if they have been created successfully. If you are in windows than your system probably does not need to be restored but rather the problem diagnosed and fixed. The problems you have may not be that bad but they are beyond the scope of our conversations here.
It sounds like the initial problem was a Windows system restore that failed . . . the clean up in particular. Do you know a knowledgeable person that could take a look at it?