I've just installed power door locks in my Honda Civic, and I've placed a fuse holder along the wire that goes from + terminal to the door lock relay.

First of all, should it be on the + side of the battery or the - side?

More important question is, how do I determine the fuse size that I need to have there? Do I have someone operate the door locks and I measure amperage being used, and put a fuse that can handle that much current? If it's using, for example, 4.5 amps, how much bigger fuse can I use? I understand I could use a 5 amp fuse, but I'd just like to know (for future reference) how much bigger (in percentage perhaps?) can the fuse be?

The wire size and the insulation of a wire generally dicates the ampacity of the wire. Since amp loads are low, and wire is not subjected to continuous heat, and circuit lengths are normally short the wire size is fine. Fusing a circuit for the actual amp draw plus 25% is what is used in building codes.

Here is a typical wire ampacity chart:

COPPER CONDUCTOR AMPACITIES, IN FREE AIR AT 30 DEGREES C
================================================== ======
INSULATION RUW, T THW, THWN FEP, FEPB
TYPE: TW RUH THHN, XHHW
================================================== ======
Size Current Rating Current Rating Current Rating
AWG @ 60 degrees C @ 75 degrees C @ 90 degrees C
================================================== ======
20 -------- *9 ----------------------------- *12.5
18 -------- *13 ------------------------------ 18
16 -------- *18 ------------------------------ 24
14 --------- 25 ------------- 30 ------------- 35
12 --------- 30 ------------- 35 ------------- 40
10 --------- 40 ------------- 50 ------------- 55
8 ---------- 60 ------------- 70 ------------- 80
6 ---------- 80 ------------- 95 ------------ 105

Thank you very much for a quick answer.