When I read any description of the Weil Pairing, it's described as a map between the additive groups $G1$ x $G2$ of an Elliptic Curve to a different group.
$G1$ is the r-torsion group of the EC curve over the base Field. i.e. $G1$ is the r-torsion group of $E(F_q)$.
$G2$ is a different subgroup of full r-torsion group of the same Curve but it would have points on the extension field - i.e. $G2$ will have points also in $E(F_{q^k})$ where $k$ is the embedding degree. $G2$ is formed by the Frobenius Endomorphism $(x,y)$ -> $(x^p, y^p)$
I understood upto this. I understood that the map ($e_r)$ constructed using rational functions & the output is a root of Unity in the multiplicative group of $E(F_{q^k})$.
Coming to the MOV attack using the Weil Pairing, the map $e_r(P,rP)$ is used to transform the ECDLP, $Q = rP$ into the DLP in the multiplicative group of $F_{q^k}$.
The question I have here is that the map takes 2 points as input. The first point in $G1$ & the 2nd point in $G2$. How do we know that $P$ is going to be in $G1$ & $Q$ is going to be in $G2$. Else this map won't work, right? What am I misunderstanding here?
I was never up to speed with pairing based attacks (caveat reader), but you seem to have some wrong impressions, so I will try and fix some of them, and share my impressions.
We fix an integer $r$. This should be selected in such a way that $E(\Bbb{F}_q)$ has quite a bit of $r$-torsion. In other words, $G_1=E[r]\cap E(\Bbb{F}_q)$ is a relatively large subgroup of $E(\Bbb{F}_q)$. I guess the normal case is that $G_1$ is cyclic of order $r$, but that is probably not strictly necessary. Furthermore, the extension degree $k$ is chosen in such a way, that the group $G_2=E[r]\cap E(\Bbb{F}_{q^k})$ is relative large. Ideally $G_2$ contains all the $r$-torsion, but that need not be strictly true. The point is that $G_2$ should be significantly larger than $G_1$. As an abstract group $G_2\simeq C_r\times C_r$ in the ideal case, but it may still be useful to use the pairing attack as long as $G_2\simeq C_r\times C_d$, where $d$ is a large divisor of $r$. Of course, if $r$ is a prime, then we need $d=r$.
The DLP problem in $G_1$ is to determine the integer $m$ such that $P=mG$, where $P$ is a given point and $G$ is the known generator referred to in the specs of the cryptosystem.
Let $e(\ ,\ )$ be the Weil pairing. It is a mapping from $E[r]\times E[r]\to \mu_r$ (from the $r$-torsion of $E$ to a subgroup of units of the extension field). Here (ideally) $E[r]=G_2$ and the group of roots of unity $\mu_r$ is a subgroup of the multiplicative group $\Bbb{F}_{q^k}$. IIRC the condition $\mu_r\le\Bbb{F}_{q^k}^*$ is a necessary condition for $E[r]$ to be contained in $E(\Bbb{F}_{q^k})$.