Can someone recommend an edition of Nefesh HaChaim? I am looking for a nice edition with clear type and explanatory notes.
I am unclear if you are looking for Hebrew or English. If the latter, then Avinoam Fraenkel has translated the entirety of Nefesh Hachaim (unlike some of the other translations which skip content or full chapters).
His translation, Nefesh Hatzimtzum comes out in two volumes and has lots of commentary, explanations and massive amount of footnotes. It is extremely clear and well-done. Volume 1 has the full translation, volume has related writings and a long essay on the concept of tzimtzum. Volume 1 has the full Hebrew text as well (newly typeset in perfect font). See the haskamot on the site as well.
Happy to share some page pictures if helpful.
Other translations into English include R Avraham Yaakov Finkel's (but there is no Hebrew and no translation of the Kabbalistic matters) and Eliezer Lipa Moskowitz's which is more complete and includes facsimiles of the 1837 edition (in ktav Rashi).
Sefaria offers the online English-version of Nefesh HaChayim from Rabbi Chaim of Volozhin. I would recommend the version/translation called "The Soul of Life, translated by Leonard Moskowitz, Teaneck, NJ 2012 [Rev. 1.5]". You can choose this by clicking on "translations".
See also this related post: English Translation of Rabbi Chaim Volozhin's Nefesh ha-Chaim?