That's mostly dependant on the base class' rules of multiclassing, but most of the time it's fine to go back and forth between the base class and PrC. The two big exceptions are druids and paladins, who once you take a different class you can't take classes in the original one without a CDQ of the character rejoining the order. (some exceptions to this include wizard milticlassing for specific Lucindite Paladin orders and Shifter which can freely multiclass with druid)
As for the more standard splits, like arcane archer with wizard and fighter or dwarven defender with fighter classes, generally you can go back and forth with the level progression all you want. The only stipulation there is that every class you have accrued must have a minimum lvl of 5 by lvl 20... so a 10AA/5wiz/5ftr split is fine in whatever order you like, or a 12 bard/8AA or 15ftr/5Weaponmaster, etc.
We do however prefer that the multiclass splits are somewhat balanced, so try to avoid applying for a fighter/wizard, then taking just one level of fighter, 15 levels of wizard back to back, then the last 4 levels of fighter at the end. Something more like 4 levels wizard per each level of fighter or so like 4wiz/1ftr -> 8wiz/2ftr -> 12wiz/3ftr -> 15wiz/4&5ftr is a more natural progression. This is so that powerbuilds dont arise, like when somebody takes 8 levels of rogue, 1 shadowdancer for hide in plain sight, then takes 7 more levels of rogue before finishing off the required 5 lvls shadowdancer PrC before 20th. It's totally acceptable though to take 8-10 lvls in a base class, get into a PrC and to want to max that PrC... so an 8th lvl fighter who goes defender may go 10 levels of defender or so to 8ftr/10defender and finish the ftr levels at the end, not too big of a gap in class levels there. Or to leave a class at its minimum of 5 levels... like 5ftr/5wiz and 10AA and arcane archer for the rest of the career. So you aren't pressured to make a 10ftr/10wiz before you hit 10AA by any means, since most PrCs are amalgams of the skills from prerequisite classes taken prior.
