Boat was laid up white with base coat / clear graphics painted. Everywhere there's graphics there's clear but not the entire boat. Where there's clear it's a snap to clean. The non cleared areas are in pretty good shape because the boat hasn't been exposed to sun for extensive amounts of time. Where the graphics stop I have diagonal lines on the side and across the deck where the clear stopped. I have a few nicks and scratches here and there that I'd like to repair. So I'm looking at 3 things:
1. Touching up the scratches and getting the clear to blend in small areas
2. Clearing the areas that don't have clear
3. Clearing the bottom to prevent staining.

How easy / practical is it to repair small painted areas and blend the new clear to the existing?
How well would I be able to clear the non cleared ares and get the line between old an new to blend?
Should I just repair the damaged areas and then clear the entire side or deck to eliminate the hassles of blending?

Lastly, Is clearing the bottom a good or bad idea?

It be nice if someone would respond to this post I have the same exact interest or should I say problem.

to clear the rest of the deck you would have to sand the hole boat and clear the complete deck. as far as clearing the bottom NOT a good idea paint does not like to be under water it blisters just use a good sealant on the gel-cote.

Any advice on repairing small nicks, dings and scratches in the clear coat?

A good painter can fix the small scratches and nicks and blend the clear. It gets done all the time by several painters at LOTO.
If the scratches are in the white, just have them repaired with gel coat.
BTW, my boat is the same way as yours, with the graphics painted and cleared and then the clear was blended into the white gel down the sides.
As it gets older, the blend has become slightly more noticeable on a cloudy day, but in the sun, you can't see it.

Depends on how small are the nicks dings and scratches. If they are small and do not go through the gelcoat, you can just sand it down. If they are deeper and go through the gel coat you might need to use a small grinder to grind the holes a little wider, patch them and then cover with new gel coat. All depends on how big are they.

DO NOT clear anywhere that is not paint/cleared already. It will blow off a few years down the road and make a mess.

If you have damage in the "graphics" repairing them is not hard. any good paint shop can do it. Where are you located?

If you have scratches in the white, those too are easy (depending on condition of gel coat) to be blended.

DO NOT clear the running surface. If anything, re paint with single stage paint.