How can I install .deb files for Cydia manually (without wifi)?

You can add .deb files and install apps from apptrackr, etc.. using the app iFunbox. I actually just used it the other day to locally upload my custom sms-tone pack. So download your needed .deb files from online, then transfer and install them via the program iFunbox.

http://www.i-funbox.com/

This might be because certain Cydia apps have other requirements. When you download an app from Cydia it checks to make sure that you have the foundational files for that app to work installed, if not then it installs them itself. If you don't have those, some .deb files might not work properly.