So I am wanting to play an Atomie they are a very small fey less than 1 foot. My DMG wants to give me like a -6 str and con or something and while I understand it is up to the DM I feel that is pretty harsh. By comparison the Pixie which is 2.5 foot tall are only given a -1 str and con per the complete book of humanoids. Is there somewhere I can find stats for creatures based on size for 2nd edition or would it be based on something else. Any help is greatly appreciated.
The Dungeon Master's Guide (1993) on Creating New Player Character Races says
Creatures of tiny (T) size have a −3 modifier to Strength. Creatures of small (S) size have a −1 modifier to Strength.… All other ability modifiers are assigned by the DM. Likely candidates include minuses to Charisma and Wisdom and plus or minus adjustments to Dexterity. In all cases, bonuses and penalties should balance out. If a creature has a +1 bonus to Strength, it should have a −1 penalty to another ability. With the exception of Strength, no creature can have a modifier greater than +2 or −2 to any score. (15)
(Note that Constitution is unmentioned.) So, while Complete Book of Humanoids does, indeed, give the pixie only a −1 to Strength, that's because of the pixie's small size. The tiny atomie, on the other hand, according to the DMG, warrants a −3 to Strength (not a −6), but keep in mind that pretty much everything's at the DM's discretion when using such a race.
Humanoids, by the way, also lists maximum pixie Strength as 14. Since the typical pixie is well over twice the height of a typical atomie, a DM that rules maximum atomie Strength is 12 isn't really being unreasonable by comparison. Were a player in one of my campaigns to've insisted upon an atomie PC, a −3 to Strength but a maximum Strength of 12 seems like an acceptable compromise over a potentially crippling flat −6 to Strength, especially if ability scores were rolled in the traditional fashion.
Based not on rules, but on physics, a humanoid a foot tall would be expected to have about 1/36 the strength of a full size person -- so instead of being able to carry a 50 lb backpack, they'd be capable of packing a pound and a half, near enough.
Compare that to D&D Strength stat, and a -6 doesn't seem unreasonable. A two and a half foot pixie would be expected, on average, to be a little more than six times as strong as your Atomie character.
Now, that said, D&D isn't very strict on physics; otherwise giants even 12 feet tall would be built more like dwarves (if they could exist at all -- a 12 foot human would weigh something like 3/4 of a ton). The best I can suggest is to work with your DM, and possibly consider playing a race for which there are available stats.