Hi there, recently I've decided to finally use a plectrum after about 2 years of playing guitar (using fingerpicking/no plectrum). I find that there is not much difference in playing, except for fast, alternative strumming, in which the pick goes down fine, but I cannot quite get the upstrum as smooth as I would like it, which puts me off my timing.

I was wondering if there was any way to ensure that the upstrum stays as smooth as the down while using a pick, and if anybody had any tips on it.
I can understand you're issue after playing with your fingers for so long. The best advice I can give you is when upstrumming is to make the tip of the pick lower then your hand. Angling it down like this will make it easier for you I hope.
Gibson Les Paul Classic
Fender Stratocaster (Mexican)
Hagstrom Ultra Swede
Music Man Axis Sport
The key, my friend, is to practice slow and steady. That's how I finally got it down (and I started out fingerpicking too); just try a four beat strum at first: down-up down-up, and go from there. Keep it up; you'll get it sooner than you think!