For your first question, no you do not get to decide how many gems your choice costs. The number of gems is determined by the number of reads a story has. You can read this link for more information about adding gem choices.
For your second question, as a writer it is potentially good to add gems because you can potentially get into the payments program quicker by only needing 100k gem reads rather than 500k normal reads (in 60 days).
If you are going to use them, I would suggest using them every chapter since it only benefits you not the reader. What I mean by that is the benefit to you is getting into the payments program so you are going to want to include the gems in all chapters to keep getting gem reads. Having gems doesn’t really benefit the reader at all.
If you are going to use gems though, be careful how you use them. Make sure using the gem choice gives the reader a good experience (ie. don’t make them feel like they wasted gems). And don’t have the use of gems take away from the quality of the rest of your story.