I need to have some applications running on specific workspaces on gnome and have the option (Always on visible workspace) ticked and remembered each time I'm loggin out. Is this possible?
There is no such option I know of in Metacity/Marco. There are, however, a handful options to ship around this issue.
Given your requirements, your best bet is Devil's Pie, as it will allow you to place the window exactly where you want it.