First off, I'd get a new doctor or see another one for this in order to have them treated. By treated, I mean frozen or electrocauterized which destroyed the wart and heals fairly quickly without scarring (at least in my experiences). Waiting a year is dumb.
Second, a condom protects the shaft. Men can still get warts on at the base of the shaft where the condom doesn't cover and on the scrotum during sex.
When you get HPV warts, most people have outbreaks of one or more warts every 6 weeks to 4 months for around a year and up to two years. During this time, sex without protection is risky because the virus, though not visible after a previous treatment, is preparing to break out again and can be transferred just as easily or nearly as easily as if warts were present because the virus is active. After a year or more of outbreaks, your immune system seems to be able to get a hold of the infection and suppress future outbreaks. If you experience six months with no new warts present, then you can be cautiously optimistic that you have reached this point. Once you'd had a year of no new warts, I'd consider myself not contagious anymore. The virus is still present, and anything's possible with HPV, but for the vast majority of HPV warts, once you've reached this stage, you may never see them again. At this point, I'd just go back to a normal sex life with giving and receiving oral and even unprotected sex (given you have the correct partner). Remember, there are many strains of both types of HPV so you are highly likely to be exposed to a different stain in the future if you haven't thoroughly vetted your partners. As a rule of thumb, I usually won't sleep with anyone who's had unprotected sex with someone else within three months of us getting together. This protects you against herpes as well.
So, to sum up, you can have condom sex during your first year or two with partners who are willing to do so once you've disclosed. Once you'd gone six months without an outbreak. Condom sex without disclosure is okay in my opinion, and after one year of no outbreaks you may return to normal behavior as if you weren't infected. I would refrain from receiving oral during up until you've got a year under your belt, too. This is just my researched opinion, though. Others might do so sooner.
When in doubt during your first year to year and a half, just disclose to your partner and see what they are cool with. That eliminates the doubt. It is possible to have a great sex life those first two years while you're waiting to put this behind you. Don't rub genitals together during foreplay, for instance. No oral. Be careful with mutual masturbation. Hands touching your vagina and then him could transfer infection. I'm not sure how likely that scenario is, but it's worth paying attention to simply to avoid anxiety. Avoid any genital to genital contact unless protection is in place and you should be fine.
Hope this helps.