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Your choices are:
1) Use calibre to send to the device. When doing this, calibre will make sure covers and metadata are up to date. It can also use plugboards to make changes some metadata. It can also create shelves and update the series info. When you next connect, calibre will know what books are on the device.
2) Use calibre "save to disk" to put the books directly on the device. This can also make sure the metadata is updated. At the next connect, calibre can attempt to match the books on the device to the calibre library, but this isn't always accurate.
3) Open the folders calibre uses to store the its library and copy the books over to the device. The metadata and covers will not be the latest unless you have done a conversion or used a plugin to update them.
If you are using calibre to manage your books, use the first option. I don't know of any problems in recent calibre versions and the 2.x.x firmware. I think people who are saying to maintain the books on the device manually, are also not using calibre for library management.
I recommend putting a few books on the device and seeing how it goes. If you don't like exactly what happens, you can tweak things before putting the next batch on. If you have a problem doing this, report it so it can be fixed or explained.
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