Filler is not your enemy, even 1/4 inch or so, not to much beyond that though will last longer that the vehicle that it's on. Main things to mention are.
1. Get all the way down to clean metal, use a quality wax and grease remover to wipe down panels before applying fillers or primers, wipe on the product and wipe totally dry with a clean cloth, wiping on a wax and grease remover and not using a clean dry cloth to wipe dry will leave a residue that you don't want.
2. Once you have clean metal you can apply filler, don't glob it on heavy, put a nice even coat with a good quality spreader, let dry then use some cheap rattle can black and mist over the filler then block it out with a 150-180 grit paper and look for low spots, the mist of black will stay in the low spots to show where you'll need additional filler.
3. When finishing your filler work Don't use a sand paper rougher than 180-220 grit, Yeah it takes longer to block it out, but the Old school guys that blocked everything out with 80 grit, were the guys that all painters hated
Today's primers weren't manufactured to be applied over a scratch any deeper than the 180-220 profile. Sure you can HOG on primer and fill anything, BUT after you paint that sucker all those Deep scratches you filled with primer will shrink forever, and you'll see Big scratches appearing in your Nice car that look really Fugly, and they don't go away until you sand them all the way down to the Bondo and reprime and paint.... Hope this helps