I have the same gun you have (a 50 cal Cabelas Hawken flintlock w/ 1:48" twist barrel - perhaps your's is percussion...), so I'll do my best to answer your questions.
If you have Triple 7 powder, you have a black powder substitute that can be used safely in black powder muzzleloaders. Goex is a brand name for real black powder. Pyrodex is a brand name for another type of bp substitute. Something to keep in mind with Triple 7, it produces higher pressures when ignited then regular black powder. Thus, it is recommended you reduce your black powder equivalent loads by 15%. For example, if your gun is rated at 120 grains maximum charge for a patched round ball - that is the recommended maximum charge for regular black powder. If you're using Triple 7, you'd want to go no higher than 100 grains (102 grains actually, which is 120 reduced by 15%). Having shot patched round balls out of a 1:48" twist barrel, I can tell you that you'll probably want to go a lot lower than 100 grains if you want the best accuracy. If you had a slower twist barrel, you could probably shoot closer to 100 grains with a patched round ball. But each gun is different, so try different charges until you find one that works well. In reality, with a 28" barrel, you're probably not burning 100% of the powder during the shot when using charges over 100 grains, thus you'd just wasting powder and not helping your accuracy.
As for the other manual recommending a lower maximum charge (90 grains?), I'm not sure what the suggest. I would go with what the gun manufacturer recommends and not exceed that limit.
If you want to try something besides patched round balls someday, give the Hornady Great Plains Bullets a try. I get outstanding accuracy with them out of my gun. 85 grains of Triple 7 and a GPB produce some very tight groups for me. Those bullets are pretty potent on deer as well, but they do thump your shoulder a bit more than round balls.
Hope this helps some,
Jeff