You asked two questions which I will endeavour to answer. Also there is a lot of documentation at the link below which might help.http://www.jdownloads.net/documentations/category/jdownloads-version-3-2
on my server i just have a folder with many sub-folders with documents, which is the best way to import all ?
As usual it all depends! There are some things that are good to check in the jD Configuration first. In the jD Configuration - Monitoring tab there are several important settings. Make sure
Download Directory Monitoring is set to No
Select whether you wish to monitor all file types or just a restricted set
If some of your Downloads are to be limited to member access only then set Automatically Publish to No as otherwise until you sort out the permissions and access they will by default be publically available and downloadable.
I assume that your top level sub folders in the present main directory will become the top level jD Categories. As they are already on the server then I would suggest the principle route will be to copy them to the jD Root directory which in a standard set up is the directory jdownloads in the top level Joomla! directory. It is possible to change what directory is the top level jD directory but it can cause unforeseen 'challenges' if you do so!!
But before you copy all in one go one has to take note that usually there is an execution time limit imposed by your website. Transferring a couple of hundered files/directories is usually ok.
But just as a caution I would sugest you copy over each toplevel subdirectory and all its 'members' one at a time. After transferring each toplevel set then go to the jD Control Panel. On the righthand side under the Staus tab you will find about two thirds down a link 'Check Download Area Now'. When you click on this jD will create the necessary database and other entries. Suggest you start with those main Categories that will have public access and permissions to Download. After creating some Downloads then see what they look like on the front end. This will bring you to the layout choices which you can see the various possibliities.
Again if you have some that require membership or other I would suggest an alterration in the premissions setup before running the 'Check Download Area Now' link. Check on setting up User Groups Settings in the documentation.
is it possible to enable a full text search for document content ? by an indexing i think..
jD does not search the source documents but you can add details into the Description part of each Download and jD doews search that as wll as Download titles.