Of course, your backlinks will still be counted. Installing an SSL certificate can potentially boost your rankings since it's now a ranking factor confirmed by Google.

yes, BUT you will need to 301 redirect all http to https, right?

It all depends on whether you create new content to go onto the https pages, or whether you do a redirect from http to https, or whether you serve the same content from both http and https.

I've ordered a rewrite for some of my pages simply because they are due to be refreshed and I'm now worried about organic than just PPC.

What are the best sources for SSL's?

I have 1 subdomain on each one.

My hosting company offers one for $99. a year which covers the subdomain.

thanks

Yes the backlinks will stay and your ranking will come back after sometime. It is also relocation of your content so need to follow the complete guidelines of the Google.
Official Google Webmaster Central Blog: How to move your content to a new location

I personally will wait for sometime because it is too confusing at the moment so it is better to wait for more detail from Google. I don't see any drastic ranking changes at the moment.