That's OK, just format them at 720k even if they're 1.4m.
For transfering larger files, you can use a few options.
One, is to use AmigaExplorer and a special null modem cable 25/9 pin and you can transfer stuff very easily between your PC and Amiga. I found my cable in a local electronic store, but they show up on ebay occasionaly.
The other is to get yourself a PCMCIA Compact Flash card adaptor. Amigakit has them.
Workbench versions for the classic machines ran from 1.2, 1.3, 2.0, 2.1, 3.0, 3.1, 3.5, & 3.9. This
PAGE has more info on that.
Oh, to format 720k PC format on your Ami, look in the Storage folder for a PC0 labeled icon. Move it into your DEVS:DOSDRIVERS folder. When you insert a floppy, a floppy icon with

? will appear, click once, choose format from the menu and that will format it so that PC's recognize it.