Where/when should I specify unsharpen when converting images to video?
Just do it all as one step and forget about up-sampling to 16 bit. That just adds complexity, processing time, extra storage and for no gain in quality in the end result that anyone could possibly perceive. 

fmpeg myinputVideo.avi -vf "scale=3840:2160,unsharp=1x=13:ly=13"la=2.0" myoutput.mp4


The internal process of ffmpeg works basically like this: 

 _______              ______________
|       |            |              |
| input |  demuxer   | encoded data |   decoder
| file  | ---------&gt; | packets      | -----+
|_______|            |______________|      |
                                           v
                                       _________
                                      |         |
                                      | decoded |
                                      | frames  |
                                      |_________|
 ________             ______________       |
|        |           |              |      |
| output | &lt;-------- | encoded data | &lt;----+
| file   |   muxer   | packets      |   encoder
|________|           |______________|


The "decoded frames" box basically is where the pixels in the image are stored in memory as uncompressed RGB or YUV (or whatever) samples. That's the point where your footage is as good as it is going to get. Any extra filtering or processing will notionally degrade the image due to quantisation loss, or compression etc.. That image is what is sent to the filter chain. What you're doing is:

demux → decode → [decoded frames] → resample → encode → mux → save → 
demux → decode → [decoded, resampled frames] → upscale → sharpen → encode → mux → save


so you're applying your filters to frames that have had an extra resample and encode step added, not to mention taking up a whole bunch'a space on your HDD.

When you filter something the output of one filter goes to the input of the next filter in the chain, so if you put scale first the scaled image is then sent to the sharpen filter. 

 _______        ________        _________        ________
|       |      |        |      |         |      |        |
| input | ---&gt; | scale  | ---&gt; | sharpen | ---&gt; | output |
|_______|      |________|      |_________|      |________|


You can get more complex by using -filter_complex which allows you to have various inputs and outputs for filters.

https://ffmpeg.org/ffmpeg.html#Filtering for more ascii-art empowered knowledge