uploading + downloading Large files ...

Hi! My users need to upload and download large files (100 + megs). Right now I only allow 100k to be uploaded. Will I need to do anything to php/apache to make sure things continue to be reliable? My google search only found threads with bad endings and they had much smaller files. Should i just make em use ftp or scp? The problem with using one of those protocols is that it makes it difficult for the users to link the files to the proper account/relation/incident and anything that is a problem for users is usually a problem for me. Thanks! Jimmy