Continue in pattern while shaping
Does that phrase put you off a pattern completely? Make you nervous about whether you're really doing it right? If it does, you're not alone! When writing patterns I try to give specific directions for every detail, but sometimes the cleanest, most legible option is to establish a stitch pattern and leave it up to the knitter to keep it going.
I find it helpful to think of allover patterns as a piece of decorated fabric or paper that I'm cutting into with my shaping. Everything should line up vertically with the fabric in the middle, not necessarily with what the stitch below the increase or decrease used to be.
A very simple example
If I was working seed stitch and had a purl at the beginning of the row if I decreased right at the beginning my first stitch would then be a knit to maintain the pattern. Decrease again and that first stitch would switch back to a knit. It doesn't matter what the first stitch has been before, it matters what is next to it in the pattern.
Shaping in lace patterns
Let's look at a fairly simple allover diamond pattern. We can tell from this chart that the pattern has the same number of stitches on every row (see this post if you're unfamiliar with charts), which means that every yarn over is compensated for by a decreased stitch.
When shaping that is the crucial thing to remember — unless you want to decrease a stitch for your shaping, every yarn over must be compensated for. If there aren't enough stitches for both the yarn over and the decrease don't work either of them. Work those stitches in your ground pattern (usually stockinette but possibly reverse stockinette, garter, seed etc).