1. One way is that you can use Methylation-Sensitive restriction enzymes for specific genomic DNA digestion to find out. This approach is by indicating whether or not cleavage is blocked or impaired by Dam, Dcm or CpG methylation. Please refer to this useful website [ https://www.neb.com/tools-and-resources/selection-charts/dam-dcm-and-cpg-methylation ] for more info. See the listed restriction enzymes in the table for their behaviors towards the sensitivity of cutting a methylated site.

2. As indicated in the NOTE, "The effects of CpG methylation are mainly a concern when digesting eukaryotic genomic DNA. CpG methylation patterns are not retained once the DNA is cloned into a bacterial host."

This is how they use Methylation Sensitive Restriction Enzymes:

[ http://www.clontech.com/takara/AF/Products/Epigenetics/DNA_Preparation/MSRE_Overview ]

"Methylation Sensitive Restriction Enzymes (MSREs) play a role in the analysis of methylated DNA. MSREs are used to analyze the methylation status of cytosine residues in CpG sequences. These restriction enzymes, as their name implies, are not able to cleave methylated-cytosine residues, leaving methylated DNA intact. MSREs cleave DNA at specific unmethylated-cytosine residues. DNA is amplified by PCR following digestion. Because unmethylated DNA is digested by MSREs, the only amplification products detected are methylated DNA. It is imperative to fully digest the DNA before PCR amplification to generate accurate data."

To validate known 5mC-sites, you can make bisulfite conversion of your genomic DNA and  design specific primers that contain your proposed methylation site at the 3' end. Now make two sets of primers, one that will work only on your methylated target and one that is specific for non-methylated primer sites. It would be good to have one  primer to match in both conditions.

or

in case your site is close to a methylation sensitive restriction site: combine a qPCR based approach with previous digestion with methylation sensitive restriction enzymes, as was suggested by Yuan-Yeu Yau  above. You then run 2 PCRs and compare digested with non-digested input. In case you enzyme cuits non-methylated DNA only, you should obtain the same amount of amplicon. At methylated sites, you should expect less amplicon compared to non-digested DNA.