scp -r source user@target:dest will walk all subdirectories of source and copy them.
scp behaves like
cp and always copies files, even if it is the same on both source and destination. [See here for a workaround.]
As this is a static website, you are most likely only making updates, not re-creating the whole thing, so you will probably find things move along faster if you use
rsync over ssh instead of
scp. Probably something like
rsync -av -e ssh source user@target:dest
...to get started. If you are doing this across a LAN, I would personally use the options
-avW instead for
Rsync also gives you the ability to duplicate deletions in your source; so if you remove a file from your tree, you can run
rsync as above, and include the flag
--delete and it will remove the same file from the destination side.