Try to do this.
1. check if your memory card is formatted using your phone formatting utility. if not, back up the files on your memory card to your computer and reinsert it to your phone and have it formatted there ( don't format your memory card from pc this is not a good idea for it).this is also a cause or one of the reasons why the files, even if you save to memory card will add to your phone internal folders. the memory card needs to adapt the phone internal first before you can use them.

to answer your question,
converting videos are not only the issues for samsung, other brands and models as well. not all video codecs are supported by 1 phone. if the manufacturers will install all the codecs for a phone player, they should install first a prom that is large enough to hold them. it's never easy huh, but look on the other side, you will learn how to convert videos not only on 1 file extensions but for many. :-)

now, to transfer files, check your phone pc connection settings, do these by selecting menu, phone settings, pc connections, and enable ask on connection, at least you can select whether you want to connect it by pc suite or by memory card. select memory card, at least on that way, you will know that your are transferring and copying files from you phone memory card to your pc and vise versa. once you had formatted your memory card, you can see the same folder as you have on your phone internals. you can easily drag and drop files.

adding videos to your internal phone, i don't believe you need to do that, but for ringing tones and alarms, the phone will immediately add them to you internal folders once you had assigned them. try going to your my files folder, and check for the files, filter them by phone and memory card. you can see the drop down list at right top hand corner of your phone and check it there if the files are there in your memory card, you don't need to copy it to phone memory. you can access the files there.
just select the files and select more for more options.

regards.