Hey, so I've owned my 1999 Honda Accord Sir-t for close to 7 months now and I love it! However the only thing letting it down is the paint. All Other panels are fine except for the hood and roof. I want to know if there are any 'cheaper' ways to fix it, or make it look some what better than it does now.

Here are some pics:

 

Roof will need to be sanded and refinished

 

How do you define 'cheap' and 'fix'? Bottom line, once the clear coat is like that it... However... my son's Accord had clear coat peeling on the trunk and around the windows. For about $20 of Duplicolor paint and clear coat it looks (bad, but) a lot better than it did.
Get some 1000 grit sandpaper or very fine steel wool and feather out all the white edges of the clear coat. For large areas start with a plastic scraper to peel it. Wipe with alcohol or thinner. Mask the edges of the panel. Spray color if you go all the way to primer. Spray the clear over the whole panel.
It's not going to look great or last for years, but it's $20 and an hour or two of time. The white peeling spots will be gone for a while (Going on over six months now and the Duplicolor is still holding up.)

 

First and foremost, that isn't the correct way to do it. If I or any other refinishing tech were to look at it, we would be able to tell you exactly what happened and know how it looks like crap. Sorry I am honest, If you want it done correctly you would need it sanded down and re finished. Honestly you could get those panels refinished and the whole car re cleared for about 1000 bucks or less if he did a lot of the prep work him self. That includes high quality clear and prep, and color sand and polish. Sure you could use cheap Dupont paint but are you really going to just cheapen out on a car like that. Not to mention where the color has been in contact with atmosphere the color is different then stuff under the clear.