- Latin America is a pretty big place with lots of variants of Spanish.
- Lápiz is, very generally, used for "pencil" only. So much so that the RAE doesn't define lápiz as anything that is usually described as a "pen".
Please have a look at this helpful forum entry, and this table for the vocabulary differences in the Spanish-speaking countries. The penultimate column contains the common words for "pen". Lápiz is used for this meaning pretty exclusively in Chile.
It's not a gerund. It's a sentence in present progressive tense, and that uses a form of "to be" plus the present participle of the main verb.
The present progressive tense in English is used a lot more often than the "estar + gerundio" form in Spanish. While English generally uses the present progressive for current or near-future one-shot actions, Spanish uses the "estar + gerundio" form if the action is in progress right at that moment, and the progression is of importance somehow.
Asking "¿Estás usando este bolígrafo?" would be a bit pointless, since it would mean that the listener is using the pen right now, while the pen is sitting next to you or in your hand (using este as the demonstrative).
Yes, they're both present tense. The one with the "ing" ending is just the gerund form of the verb.