Go all in and get dedicated cycling boots. I did the toe cover route for a couple of years and the neoprene shoe cover route for a number of years. Once I got Lake boots (MXZ303 and MX145), I won’t go back.
A couple of things to do if you want to stubbornly stick to toe covers:
1. Thick wool socks. If it’s really cold, go for
over the knee socks.
2. Bigger shoes (one size larger, at least) to accommodate the thicker socks like Nyah suggests
3. If using cleated shoes, cover the cleat holes with aluminum furnace tape. Seals up the holes and the aluminum reflects heat a little.
4. Get insoles with aerogel insulation
like these. Far better insulation than just about anything.