Multistore and SEO still unresolved

[clubvapea]

I know this is a pretty beaten topic, but after hours and hours of researching I can't quite find a solution.

My case is the following:

 

1. Primary store "clubvapea.es" selling ecigs. Available in almost 10 languages.

2. A newer and better version of the store, with same products. "http://xn--shktupakka-nikotiininesteet-bkc83c.com/", available in many languages as well.

 

They are under the same shop group, but set as two different shops, with different themes. Now, the second store is set up as an ALIAS for clubvapea.es under my hosting. Only the first site shows up in search results. 

 

How do I get my second store to show up as well? In what context could I get penalised for duplicate content?

 

And another question. I want store 2 to have different URL's for different countries, only having one language per URL, and to show up in the search results with the different domains. I have got .com, .co.uk, .de domains with different names for this purpose.

 

Please help me! Thank you