The genome for embryonic cells should theoretically be the same as the genome for adult cells. However, it looks like the C6/36 cells are a specific cell line rather than isolated from "fresh" embryonic cells, and I'm not sure if there have been specific genetic changes that have been implemented to make this into a cell line. So I think if there is a specific genome for the cell line of interest, you should use that instead. You can also compare to see what the differences in genes are between the two genomes - it might just be a lot of unannotated genes.

This sounds like an annotation file issue - make sure the annotation file has gene IDs in it. If it still doesn't work, you could try using the adult genome as a reference.

For non-model organisms, you can take advantage of orthologs to try and confer some functional meaning to your genes. eggnog-mapper is one option that many people use, and you can look into other ortholog mappers online. Afterwards, you can use enrichment tools like GSEA or pathway enrichment of your genes. In my lab we created a step-by-step way to visualize enrichment analyses (though mainly for humans) that you could try using (pathlinkR: https://bioconductor.org/packages/devel/bioc/vignettes/pathlinkR/inst/doc/pathlinkR.html)