Are undergraduate journals a good choice for publishing papers?
Don't publish in weird journals 

Work to publish in the mainstream journals, despite their fickle biases and sometimes burdensome cost. Fields often have a pecking order of journals and the journal in which an article is published can change the perception of an article. Journals such as the national high school journal of science may be well-intentioned, but seem to provide a way for people to start worrying earlier and earlier about publishing.

It is premature for you to worry about your publication profile.

You've already published one paper at 16-- that's great. You are ahead of the curve. Graduate programs look for undergraduates to have published. Colleges look for evidence of potential. In the two labs I've worked in, the PI evaluates prospective high school students and undergraduates based on a letter of recommendations and a brief talk with the prospective student. Incremental publications in third tier journals may be a necessary part of the tenure slog, but you have the time now to just learn science and decide whether you want to pursue it as a career. Worrying about publications in high school is putting the cart before the horse.