The fuse or fusible link needs to be sized according to the gauge of the wire it will be protecting.
The general rule for fusible links is to use a link that is 4 wire gauge numbers smaller than the wire. Some will say 2 sizes smaller because AWG skips odd numbers. So for example you would use a 14 gauge fusible link to protect a 10 gauge wire.
And here is a link to a chart that shows the recommended fuse sizes based on the wire gauge -->
http://bdfuses.com/fusesnwires.php So using the same 10 gauge wire for example, you would want to use a 30A (maximum) fuse.
For protecting the main feed wire(s) in your new harness, you'll want to locate the fuse(s) or fusible link(s) on the end(s) of the wire(s) near where they connect to the battery.