For example if I have ODE where $x$ is a matrix of $x_1$ and $x_2$ $$x_1 ' = x_1 - 5 x_2$$ $$x_2 ' = x_1 - 3 x_2$$
and I found the solutions which are $$x_1 = c_1 e^{-t} (2 \cos(t)-\sin(t)) - c_2 e^{-t} (2 \sin(t)+\cos(t))$$ $$x_2 = c_1 e^{-t} \cos(t ) - c_2 e^{-t} \sin(t)$$ $c_1,c_2$ are constants
Now I know that due to $e^{-t}$, it will have decaying solution as t goes to infinity and will be unstable spiral that is moving in clockwise direction. However, my question is about $c_1$, $c_2$, what do these $c_1$, $c_2$ represent in the phase portrait?




Those constants provide information regarding your position at time $t = 0$, and further they are entirely dependent on that initial condition. Notice that when you plug in $t = 0$ into your equations for $x_1$ and $x_2$, you are at the point $(c_1, c_2)$.