I've just hit lvl 2 on my bard but I was wondering if dndbeyond automatically calculates the half proficiency bonus or would I have to do that myself? So for example if my char sheet says I've got a +2 on medicine and I were to roll a check  for medicine , would I get a +2 or a +1 as the bonus? I tried to google it but couldnt find a clear anwser. 
Thanks! :)

D&D Beyond automatically calculates that. You can just use the bonus as shown for each skill.

It even adjusts initiative since it as “an ability check you make that doesn’t already include your proficiency bonus.”

Beyond doesn't however add it to the six basic ability checks - it adjusts the number and rolls with the bonus on all non-proficient skills and initiative, why not on the base ability checks?

Quote from Mike_D_Summers >>

Beyond doesn't however add it to the six basic ability checks - it adjusts the number and rolls with the bonus on all non-proficient skills and initiative, why not on the base ability checks?

They probably should, but from a programming perspective, it was probably easier (and cleaner) to just leave the base ability checks alone.

Plus... I have a gnawing suspicion that there's SOME time or another where you'll need to roll an Ability check on the sheet and need to add the modifiers yourself, and they didn't want to interfere with that.