"Nobody else can do it for you." - Never a truer statement made, when it comes to modding "your own" game.
Personally, I wouldn't let LOOT touch my FO3 game, but maybe that's just me. FO3Edit (xxxedit) is your one true friend when it comes to modding. If you don't know how to use this program in it's entirety, you're shooting shadows in the dark. It's the only certain way to achieve a pristine load order, with zero conflicts. After all, load order is all about conflicts... nothing else. I'll take xxxedit over LOOT, BOSS, or anyone's voodoo opinions on what should go where. Running a "conflict report" in xxxedit is your one saving grace. Enough said.
WryFlash is another program that's a must. If you're not bashing (bash tags) your mods together, then you're a noober. Also, one click and all your Form IDs are dealt with too. I mean, unless you're using something like WMK, with it's plethora of Form IDs... then I could see using a merged patch. Bleh
I'll do a bash patch over a merged patch any day of the week. I've seen a merged patch make a complete mess of leveled lists with certain mods.
Everyone has their own preferences. To each their own. However, this is not a plug-n-play activity. I said that earlier. I'd start off with some simple things first. Don't try and download all the top 100 mods and get them to work. Been there, done that. Doesn't work. There's a serious learning curve to modding games. It's why I started you off with that link above. Unfortunately, a lot of the tutorial stuff on this game is a tad dated, but it's still got some value to it. Check out some of Gopher's old youtube videos while you're at it. They may help too. Like anything you mess around with... the more you f*** with it, the better you know it.
(Pro Tip) The top 100 mods isn't all that accurate any more. Do some filtering. There's new stuff that's better, but don't have the ratings of yesteryear. Just sayin'.