citizenship by naturalisation or by marriage

I'm wondering if I've made a mistake ticking the box where I said I'd apply as a spouse of a British citizen. I've been told that I didn't need this as I'm an European with a residence card and I can show my own employment and living records. Furthermore I can't find my marriage certificate and the only document I have to prove it is a Spanish family book (in Spanish). Will they accept my documents as an European with residency exercising treaty rights by myself even if I ticked the spouse pathway? thanks

Do you hold a document Certifying Permanent residence. This is different to a residence card.

Yes, I have a document certifying permanent resident (for a national of an EEA state). I guess my options are- 1 ask the home office if my application can be in my own rights as Foreigner livinging in the uk and not as a spouse (all valid documents sent out this morning) or 2 wait until I have a marriage certificate re issued and translated and send it over. I don't know if they'll allow any of the options. I'll try to talk to them. any advice?