I want to show you that the choice of up or down as the positive direction does not produce conflicting results.
Suppose you choose up $\hat z$ to be positive.
Think of all your vector quantities as components in the $\hat z$ direction so any downward vector would be in the direction $-\hat z$ or have a negative component in the $\hat z$ direction.
$\vec F = m\vec a\, \Rightarrow \, -mg \hat z = ma \hat z \, \Rightarrow \, a = -g$.
The component of the acceleration $\vec a$ in the $\hat z$ direction is $-g$ and so the direction of the acceleration is downwards.
The frictional force is $-bv \,\hat z$, with the sign of the component of velocity $v$ in the $\hat z$ direction switching sign when the direction of motion of the particle changes and this in turn switches the direction of the frictional force.
You must not prejudge the direction of motion of the particle rather set up the differential equation and solve it to find the component of velocity in the $\hat z$ direction as a function of time.
The equation of motion is the same for the particle going up and for the particle coming down.
$\vec v = v \hat z \, \Rightarrow \, \vec F_{\rm friction} = -bv \hat z \,\Rightarrow \, -mg \hat z -bv \hat z = ma \hat z\Rightarrow - mg - bv = ma$
Note that when the particle is going up and the component of velocity in the $\hat z$ direction is positive the frictional force is in the downward direction and when the particle is going down and the component of velocity in the $\hat z$ direction is negative the frictional force is in the upward direction.
This is exactly what you want to happen?
Now suppose you choose down $\hat z$ to be positive.
As before $\vec v = v \hat z \, \Rightarrow \, \vec F_{\rm friction} = -bv \hat z \,\Rightarrow \, +mg \hat z -bv \hat z = ma \hat z\Rightarrow + mg - bv = ma$
Note that the direction of motion of the particle has not been chosen ie the component of velocity of the particle $v$ in the $\hat z$ direction might be positive or it might be negative.
If the component of $v$ is positive it means that the particle is moving downwards and the frictional force is upwards.
If the component of $v$ is negative it means that the particle is moving upwards and the frictional force is downwards.
The final solution for the component of velocity in the $\hat z$ direction only differs by a sign as to whether $\hat z$ is chosen to be up or down.
The component of velocity in the $\hat z$ direction at a time $t$ is given by
$v(t) = A \exp \left (-\dfrac {bt}{m}\right )\pm \dfrac{mg}{b}$
the constant $A$ being determined by the initial velocity of the particle.
When it comes to the initial velocity $\vec v(0)$ it is easier to have it as either $v_0\,\hat z$ or $-v_0\,\hat z$, depending on the initial direction of the particle and the direction of $\hat z$, and with $v_0$ positive.
Note that as time $t \rightarrow \infty$ then the component of velocity in the $\hat z$ direction tends to $+\dfrac{mg}{b}$ if $\hat z$ is down and $-\dfrac{mg}{b}$ if $\hat z$ is up.