yes that will be a big problem - cardinal rule, that is repeated everywhere on these forums and wiki, do not mount or symlink anything! No, just don't! Stop it! Right now!!
Partition and format your drive with ext3, then install it in your core and wait for LMCE to detect it and prompt you what to do with it. Tell it you want to use the LMCE folder structure and to use it automatically. LMCE will then do all the automounting and symlinking needed to present it to your core for media, and to all other MDs in the house completely transparently. If you attempt to mount or symlink it yourself, you will break LMCE's storage management mechanism (probably permanently!)