I have checked in ENS platform, web control, threat prevention, firewall (10.5.1) and McAfee Agent 5.0.5. I can't seem to update in Software Manager because components failed to check in.
They are instantly failing, which is why I manually downloaded and checked in the packages from McAfee download's page, and then upgrading the respective products. Am I doing it incorrectly?
No, you're not doing it incorrectly. Manually downloading and uploading to ePO is common practice.
It sounds like you're being blocked from connecting to McAfee from ePO(Software Manager).... I'd take a look at FWs first, run a packet capture if you can from ePO Server. I'm pretty positive its a network issue.
Click "Refresh" in Software Manager and see if that does it. Although, newly released minor versions are not always accessible immediately via Software Manager. You may have to download from internet.