Metal Gear Solid Story

Solution 1:

So I am very confused on this, there are two snakes?

Five, actually. Unmarked spoilers ahead.

Big Boss (Naked Snake) is the original Snake. He is the main protagonist of MGS3. The other Snakes are cloned from or based off him.

Solid, Liquid, and Solidus are imperfect clones made by the "Les Enfants Terribles" Project.

Solid Snake is the protagonist of MGS1, part of MGS2, and MGS4. Usually, "Snake" refers to him. Unlike his brothers, he is almost identical in appearance to Big Boss.

Liquid Snake was killed in MGS1. Revolver Ocelot stole his arm and had it transplanted to replace his, which he lost. Liquid later took control of Ocelot through this arm to become Liquid Ocelot.

Solidus Snake appears in MGS2.

The Snake in MGSV is Venom Snake, a body double of Big Boss. He is not a clone- the resemblance was created by plastic surgery so he could impersonate Big Boss.

Solution 2:

It might help if you look at the series timeline to get to grips with the Snakes:

1964 – MGS3: Snake Eater
1970 – Portable Ops
1974 – Peace Walker
1975 – MGSV: Ground Zeroes
1984 – MGSV: The Phantom Pain
1995 – Metal Gear
1999 – Metal Gear 2: Solid Snake
2005 – Metal Gear Solid (The Twin Snakes)
2007/09 – MGS2: Sons of Liberty
2014 – MGS4: Guns of the Patriots
2018 – Revengeance

There are a few Snakes that fall into this timeline:

Naked Snake

MGS3 (1964) to MGSV (1984)

aka Big Boss aka Venom Snake

MGSV Spoiler:

Venom Snake turns out to be a body double of Big Boss, and actually not related.

Solid Snake

Metal Gear (1995) to MGS4 (2014)

Genetic clone of Naked Snake.

Liquid Snake

Antagonist of MGS1 (2005)

Genetic clone of Naked Snake.

MGSV Spoiler:

Appears in MGSV as a child called Eli

Solidius Snake

Antagonist of MGS2 (2009)

Genetic clone of Naked Snake