I am conducting DEG analysis with many different treatments and controls and am told that the control plasmid has background effects that we don't want to see as differentially expressed genes in any comparison with or without the control plasmid samples. Is there a way to provide RUVSeq the samples that we think would cause unwanted variation, instead of it calculating it by itself? Could you direct me to the appropriate literature, to learn how I could do this?

I think it will capture it automatically. E.g. if you use the method that focuses on genes lowly or not affected by the treatment, then the factors should capture background effects I believe.

If you have a way to identify "background effects" you can run RUV and then look at the factors and see if they seem to correlate.