Regarding supplies.

I have a question regarding supplies (life,armor,ammo,etc), is it necessary to have it just scattered in the entire map? or make a special room just to resupply for the next two or three large sectors?

Suit yourself. Whatever is better for you. Both are okay.
But if they're scattered, some dumbass will complain about being too dumb to see them, and if they're concentrated, some dumbass will complain about being too dumb to get back to the supply closet. Bear that in mind :]

There are no hard rules. Use pickups to shape the experience you'd like. Also keep in mind that all pickups can have not only a survival-oriented function but also a diegetic role. Think for example of a crate room stuffed with rocket boxes and medkits, or a trench that has lots of single shotguns next to player corpses. Pickups influence aesthetics in quieter ways too: imagine the difference between stimpaks scattered around loosely and medkits arranged in neat clusters; think of that soulsphere sitting so appealingly on a structure that seems to have been designed specifically for it.

If you are aiming for smooth flow, you can place pickups in a way that minimizes excessive backtracking for supplies. A long and "stringy" map for example might be best served by concentrating pickups some distance from the numerous action hotspots, instead of just placing them in some special storage room near the start. But of course you still have some freedom to arrange these the way you want.

I think one of the most exciting moments in Doom is when you get seriously hurt and start running around the previously visited areas in panic, hoping that there are still some stimpacks you didn't use. From that point of view scattered supplies are a lot more interesting.

I think it's really exciting when you are getting hurt and picking up stimpaks and medkits scattered around in a desperate bid to survive. It's also fun when there is a more highly guarded oasis of health (a few medkits, or a soulsphere) and you have to clear out monsters to get to it, forcing you to decide whether to prioritize the higher-threat monsters roaming around and subsist on the scraps, or take out the lower-threat guardians of the health and risk losing lots of momentum. So yeah I think scattered supplies are a good default, with occasional larger stashes serving as big rewards or strategic hot spots. :)

There's nothing like that sigh of relief from finding a berserk pack secret or one of those WOLF3D style secret closets with the 50 medical kits in them though.

Anything can work well if done right, and anything can be annoying if done wrong. If you want the player to have it easy, feel free to place supplies all around the map. If you want the player to have it hard, feel free to not place any supplies into an area where a difficult battle takes place. However, I'd recommend not to place supplies in huge amount of small pickups with each pickup in its own alcove, because having to visit a huge amount of alcoves one-by-one is rarely not annoying. Better allow the player to collect a group of pickups comfortably, that is, without it taking too much time.