I've done some LFR and I know once you loot a boss in LFR, you can't loot them again if you queue for LFR unless you have a token. So here is my question. Lets say I want to join a Flexible raid or just a normal 25 man guild raid. Will I not be able to obtain loot since I already looted the bosses in LFR queue? Or is LFR/Flexible/Normal/Heroic all separate
Flex works the same way as LFR, which you already understand.
Normal and heroic share a lockout, as stated above, so you can only kill a specific boss on normal or heroic once per week. Bosses in normal and heroic drop a set amount of loot (two items in 10-man, six in 25-man). The items they drop are randomly selected from their loot tables and the raid has to decide how they want to distribute the loot. Some guilds just let people roll for the items they need, others leave the decision up to a loot council and others use point-systems to reward players for loyalty or even out the distribution of loot over time. You should ask the raid leader to clarify loot distribution rules if you join a raid and don't know them.
If you haven't done any normal mode raiding before, the lockout system may be confusing. If you join a normal raid and kill 3 bosses, you are "saved" to those bosses and cannot fight them again until raids reset on Tuesday. If you try to join another raid which hasn't killed those three bosses, you will be unable to enter the instance; or, if you're the first one in, they will be unable to and in either case, they are probably not going to be happy with you for wasting their time. However, you CAN join another raid that has already killed all of the bosses you have killed, and you can skip bosses to do so. So, if you killed the first three bosses but you get invited to join a raid that has killed five bosses, you can enter their instance and fight the sixth boss together. However, if you defeat the sixth boss, you will be saved to all six bosses and you cannot go back and kill bosses four and five again. To make this even more incomprehensible, you will get saved immediately to the lockout of any heroic raid you enter (after agreeing to it by clicking "accept" on a pop up).
So you can have three chances at loot for any given boss in one week: 1 chance from LFR, 1 from Flex and 1 from either normal or heroic. Obviously, the harder the difficulty setting, the better the loot.
Normal raiding, and even flex to an extent, is a very different world than LFR. If you want to get into organized raiding, you would do well to find an established guild. Tell them you're new to it and find a guild willing to help you learn the ropes. Good luck.