how to wire BC547 LED flashing circuit in EAGLE?
This is actually pretty simple! Just flip R2 around. Then you can put it as "bridge" over the net that is labeled N$4 in your layout. (That's not even necessary, you can just put the trace between T1's first and third pin.)

Exactly the same for R1: use it as a bridge over N$5, i.e. route N$5 under it. 

The rest is no problem at all, you just haven't routed it yet.

Board design takes a little practice, so after you solved this, look at it intensely and find all the ways you could have arranged this "nicer" by doing things such as making traces straight, rotating or shifting components, and so on. 

For example, your placement of C1 and C2 is pretty inefficient. 

EDIT: Since you're asking: