Not exactly the universe. They pop out from the vacuum as real particles (on-shell particles) because the available energy is enough.
I don't exactly understand the rest of the question, you had 1 pair of quarks, let's say [itex]q \bar{q}[/itex]
and you move them away (since latex doesn't help, allow me to write [itex]\bar{q}[/itex] as q*)
q---q*
q--------q*
q----[q* q]---q*
(qq*)+(qq*)
In [..] I put the popped up quarks... So what do you mean by matter or antimatter? In the first place you can't have a particle consisting of two quarks. The least are the mesons consisting of [itex]q \bar{q}[/itex] and then are the baryons consisted of [itex]q q q[/itex] In the case you try to move away a quark from a baryon, you'll most probably get a meson out.:
qqq
qq---q
qq------q
qq---[q q*]--q
(qqq) + (q*q)
This happens because of the properties of QCD... In electomagnetism, taking two charges away from each other, the energy density between them gets dispersed and so weakens...In QCD though the picture is different, and it looks like a string (no wonder string theory was first proposed to explain strong interactions). The energy density between q and q* gets concentrated around their distance (more correctly the potential becomes that of a string), and if it gets enough [qq*] can be created.