When somebody says 'welcome' in english they usually mean 'i welcome you' but don't say the whole thing; just saying 'welcome' instead. In Czech, formally you should say "Vitame Vas/Vitam Vas", or in a friendly way you should say "Vitame Te/Vitam Te." If it's only one person DOING the welcoming, then use vitame; if more than one then use vitam.

The phrase 'vitejte' can also be used, but the answers I just proposed are better in my opinion.