Learn Portuguese (Portugal): Ele deita o lápis na gaveta.

To say "is laying", you use the verb estar (to be) plus a and the dictionary form (infinitive) of the main verb, which is deitar. For ele (he), estar becomes está. So, you would change the sentence to: Ele está a deitar o lápis na gaveta.

The word lápis ends in an "s". How can we tell he is only laying down one pencil?

The noun lápis is spelled exactly the same way in both the singular and the plural. You have to look at the word right before it: the singular masculine article o (the) tells us it is just one pencil. If it were multiple pencils, it would be os lápis.

Why does the sentence use "na gaveta" instead of just "em a gaveta" for "in the drawer"?

In Portuguese, the word em (in/on/at) almost always merges with the word for "the". Because gaveta (drawer) is a feminine noun, "the drawer" is a gaveta. When you combine em + a, they merge to form na.

Does the verb deitar always mean "to lay"?