So gave this game another chance and i wonder where can i store items in which containers?
I joined a few guilds as a high elf one of them is the mage guild in balmora,there i wonder if i can store my items in the chest where i got the magicka potions,you know the chest that the mages guild shares with you at least no one was shouting thief when they seen me.
Just wonder if some containers reset that i shouldn't put my items into it.

I don't believe containers reset at all or if they do its a very rare thing in Morrowind.I think the guild chests are one of the few examples of respawning containers in Morrowind.For player storage you either use a mod the adds a player home of which there are many.Or find a house that you can make your own here is a list of suggestions.

[url=http://www.uesp.net/wiki/Morrowind:Houses]http://www.uesp.net/wiki/Morrowind:Houses[/url]
on the mod front I would check Morrowind Nexus,Great House Fliggerty or Morrowind Modding History and for video demonstrations Dark Elf Guy on youtube has video series called Morrowind Modding Showcase which always includes a house mod in its regular showcases.

Since you're already in Balmora, check out the [url=http://en.uesp.net/wiki/Morrowind:Balmora_Homes#Hlaalo_Manor]Hlaalo Manor[/url]. Inside you'll find the corpse of mr Ralen but don't worry -- you can use the rest of the house to store your stuff. You can even use the corpse to store your stuff!

Generally, the containers in Morrowind don't reset but be careful with them because if you use one that belongs to an NPC, when you try to get your stuff back you'll have problems (that's the reason you already have some problems). It doesn't make sense, but then again.. it does!

If you don't mind using mods, you can also download a house mod. ;)

Ok thanks for the info,marked as solved and i don't really want to use a house mod i think the mcp patch is enough with prevent assasin attack and fix rumors.
Was a hard time deciding who to mark as solved but too all thanks for info.
Also do stolen items in chest also dissapear if i get arrested?

The corpse of Ralen Hlaalo is the best container. Infinite capacity, doesn't reset, easily found, available since the very beginning of the game.

There's a bunch of containers that do reset, not just guild storage. Generally, do not trust outside containers (like the pots that are in the streets). And stuff left on the ground can disappear if the cell itself reset.

When I took the slave to the drug runner's house he killed the slave. After he gave me an enchanted ring I killed him, and now his house is mine. So I store all my goodies there.