Be careful - about sustituting components on packaged PC systems. There can be problems with proprietary/non-standard motherboard designs on packaged PCs.
At the very least, be very certain that the power sockets on the motherboard are wired to standard pin-out conventions. If not - up in smoke!
My suggestions:
- If your PS is adequate and problem-free, leave it alone.
- While the e-machines system may be 'upgradeable', I'd think instead about 'replaceable'.
If I read your post correctly, you're considering replacing PS and adding an AGP card. I'd add a new motherboard to the list - assuming the e-machines case can accomodate standard motherboards (size, stand-offs, back-plate).
Hope this helps!