What I did was went to the File Manager or the Database Manager (as appropriate), and used the upload button.
You can then upload you files 10 at a time.
Be sure to upload only the .aspx, .aspx.vb, web.config, web.sitemap, site master and .aspx.cs files as well as the database files as well as graphics, etc.
Do not use "show all files" and upload the rest of the files. It is unnecessary and may cause significant problems.
I setup my VS 2010 setup to use database instead of App_Data as the location for my database to help.
Also, if you use classes for either VB or C#, you need to create a component (.dll) file and upload it because the import or using statements do not work with uncompiled code on this site like they will in VS 2010.
A .dll file created for VB will work for C#.