Question about excersize

 It feels like I pulled a muscle over the top of my foot (where you lace your shoes).
The question is do I stop excersizing and wait for it to heal or keep going? 

I use one of those tight ankle braces on my left foot and ankle. (I broke it 20+ years ago and it still gives me fits!)  I'd think you could do what you can, but if it hurts, quit!

Maybe you could adjust your exercise routine until it heals? Instead of running, walking, treadmill, etc. , you could bike or do resistance?

I'd try wrapping it and see if it helps at all.

 For some odd reason it only hurts when my sneaker is on

Mine are like that. I have super high arches and it causes my shoes to kinda press on the top or something and it hurts. I just try to ignore it as long as I can! (I'm sure that isn't the best option! Ha!)

Maybe you could get some socks that are more padded or something.

You might try going to a running store and getting fit for shoes.  They will look at your stride and any areas you are having problems with and make a suggestion.  It is well worth it.

Personally, I'd go to a doctor before I'd get advice over the internet. Even if someone here knows what they are talking about (and many do), we can't see or feel your injury. You could have just bruised it and need to rest it and put ice on it or you could have broken something.

In general, though, you shouldn't workout through either of those kinds of injuries. You do RICE which is

R - Rest
I - Ice
C - Compression
E - Elevation