I've taken over the corner of the counter too - now hubby has joined in!! We have a 2.5 ft section of the counter covered in pills or herbs! LOL!
I use my phone alarms to know when to take things, and would write on the top of each bottle how many times a day and how many/much each dose.
I have these little dose cups that come with things like children's tylenol or other things - and I use those to set my pills out daily.
When I was doing medicinal teas, I would put them in one of those 'safe' water bottles, and would mark on it how much to drink for each 'dose'.
When I finished something or needed to take a break from something for some reason, I would write it on the calendar, along with any changes I made.