Depending on the make of your new hard drive. You should have either software ( if purchase was retailed boxed ) or be able to download software from the hard drive web site to clone the entire old hard drive to the new one.
Yes that what you do and set the jumpers at the back to slave. if it's not recognised in windows you may have to go into bios and auto detect the drive and save the settings when you exit. if you are win 98 just go into explorer and right click the drive and choose format. just like a floppy disc