you have noticed that digital levels are hotter than analog levels. One reason for this is that most "mastered" CD's attempt to utilize all of the available headroom and many times to operate entirely within the range denoted as "headroom". My mixdown deck probably clips at +22 db so it has more headroom than my digital converters...yet the average level is still low for normal material, and music doesn't come close to clipping the converters.
So you have two options. The first is to record at normal line level at 24/96 (or 24/44), and then normalize, dither and covert to 16/44. This should ensure that your volume level isn't above optimal operating conditions for your converter, especially if you don't have the best converters. Just because the converters aren't clipping doesn't mean they're at their most linear response. With 24 bits, you could burn some db's and still be in the clear.
The second option is to insert a piece of gear with some good clean gain (or colored if you prefer that) between the 2-track and the ADC, and capture at 16/44 already dithered. This is what I do...eq and compress between the 2-track and the converters, monitoring through the converters. That is the key, for me. When mixing, I monitor the repro head of the 2-track, and when mastering, I montor the digital signal. This allows me to eq and listen to exactly what the final product is. This to me, is the downfall of anyone trying to master for mp3's, because I do not know of a way to listen "through" an mp3 coverter, as you are tweaking. So my chain goes 2-track -> eq -> compressor (light with good gain) -> ADC @ 16/44.
Both options are commonly used AFAIK.