Let's say Im playing a multi-class wizard/fighter, I get to the point of prestige classes (for this example this would be level 6 ) and go into eldritch knight for 5 levels, but for my 12th character level I want to go back into wizard... does this make me a 9th level wizard, thus loosing out on any bonus feats, save and base attack bonuses I would have gotten if I would have stuck to straight wizard? Or would I go back to 6th level wizard and then progress normally in that class having to either suffer through "x" amount of dead levels before I gain new spells again or double up on spells from those spell levels?
You don't get any class features from a spellcasting class when you take a prestige class unless the PrC says you do so those bonus feats are lost.
In short you lose out on anything the class would give you.
Neither. Let us say you are a Fighter 1 / Wizard 4 / EK 5. When you add a level wizard, you would become Fighter 1 / Wizard 5 / EK 5. You gain a bonus feat for hitting Wizard level 5, any BaB or save increases (none, in this case), and your spellcasting level would go up by 1. Just like any other multiclass.
The only difference would be, because of your EK levels, you would be going from casting spells as a 8th level Wizard (4 Wizard levels + 4 increases from EK) to casting as a 9th level Wizard (5 Wizard + 4 EK). This does not in any way relate to your BaB, saves, school powers, or other level dependent variables. There are no "lost" levels, nor do you double up spells or anything of the sort. A character who went from Fighter 1 / Wizard 5, then gained 5 levels of EK, then a level of Wizard is in no way different from one who waited until Fighter 1 / Wizard 6 before switching to EK.
I hope that clears things up a bit.
+1 to what the previous posters said :-)
Just a note about your progression: You must be at least figher 1/wizard 5 to enter EK, so level 7 is the earliest possible.
Fighter can be exchanged for other classes with all martial weapon proficiency like ranger of course.
Carefully consider if you want EK. It is a cool prestige class, but it has its problems. Sometimes the magus class, arcane duelist bard class or arcane archer prestige class are more what people are actually aiming for :-)
I cosign what the other 2 posters said. What you have to decide is do you want to be a caster who can fight or a fighter who can cast.
Thanks everyone, that makes alot more sense now