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I'm going to crop some desktop regions and overlay them on the scene.

avconv -f x11grab -s:v 100x100 -r 30 -i :0.0+10:10 
-f x11grab -s:v 100x100 -r 30 -i :0.0+200:200 
-f alsa -ac 2 -i pulse  
-c:a libvo_aacenc -b:a 96k -ar 44100 -ac 2 
-vf "color=black@0.8:1366x768:30, setpts=PTS-STARTPTS [BLACK];
    movie=/dev/video0:f=video4linux2, vflip, scale=240:-1, setpts=PTS-STARTPTS[CAM];
    [BLACK][in] overlay=0:0 [BLACK+in];
    [BLACK+in][CAM] overlay=1000:10 [out]" 
-c:v libx264 -preset veryfast -crf 22 -b:v 512k -bufsize 3000k -threads 0 
-f avi -y ScrVideo.avi

But it doesn't work and i don't know how to separate "Input #0" and "Input #1" in filter. Docs are very strange and everywhere only "[in]->[out]" scheme has been used. The result is black scene with camera. I tried to sprit the whole desktop (1366x768) on 2 pads inside the filter and crop regions there but it doesnt work too.

avconv version 0.8.10-4:0.8.10-0ubuntu0.12.04.1, Copyright (c) 2000-2013 the Libav developers
  built on Feb  6 2014 20:59:08 with gcc 4.6.3
[x11grab @ 0x9ce43c0] device: :0.0+10:10 -> display: :0.0 x: 10 y: 0 width: 100 height: 100
[x11grab @ 0x9ce43c0] shared memory extension  found
[x11grab @ 0x9ce43c0] Estimating duration from bitrate, this may be inaccurate
Input #0, x11grab, from ':0.0+10:10':
  Duration: N/A, start: 1396538114.117124, bitrate: 9600 kb/s
    Stream #0.0: Video: rawvideo, bgra, 100x100, 9600 kb/s, 30 tbr, 1000k tbn, 30 tbc
[x11grab @ 0x9cf3860] device: :0.0+200:200 -> display: :0.0 x: 200 y: 0 width: 100 height: 100
[x11grab @ 0x9cf3860] shared memory extension  found
[x11grab @ 0x9cf3860] Estimating duration from bitrate, this may be inaccurate
Input #1, x11grab, from ':0.0+200:200':
  Duration: N/A, start: 1396538114.154109, bitrate: 9600 kb/s
    Stream #1.0: Video: rawvideo, bgra, 100x100, 9600 kb/s, 30 tbr, 1000k tbn, 30 tbc
[alsa @ 0x9d0ce40] capture with some ALSA plugins, especially dsnoop, may hang.
[alsa @ 0x9d0ce40] Estimating duration from bitrate, this may be inaccurate                                                           
Input #2, alsa, from 'pulse':
  Duration: N/A, start: 1396538113.995116, bitrate: N/A
    Stream #2.0: Audio: pcm_s16le, 48000 Hz, 2 channels, s16, 1536 kb/s
Incompatible pixel format 'bgra' for codec 'libx264', auto-selecting format 'yuv420p'
[buffer @ 0x9d2ca00] w:100 h:100 pixfmt:bgra
[video4linux2 @ 0x9d21660] Estimating duration from bitrate, this may be inaccurate
[movie @ 0x9d21320] seek_point:0 format_name:video4linux2 file_name:/dev/video0 stream_index:0
[overlay @ 0x9d2dae0] auto-inserting filter 'auto-inserted scaler 0' between the filter 'src' and the filter 'Parsed filter 6 overlay'
[color @ 0x9d0fd00] w:1366 h:768 r:30/1 color:0x108080cc[yuva]
[color @ 0x9d0fd00] TB:0.033333
[scale @ 0x9d2ec60] w:100 h:100 fmt:bgra -> w:100 h:100 fmt:yuva420p flags:0x4
[overlay @ 0x9d2dae0] main w:1366 h:768 fmt:yuv420p overlay x:0 y:0 w:100 h:100 fmt:yuva420p
[overlay @ 0x9d2dae0] main_tb:1/30 overlay_tb:1/1000000 -> tb:1/3000000 exact:1
[scale @ 0x9d22260] w:640 h:480 fmt:yuyv422 -> w:240 h:180 fmt:yuva420p flags:0x4
[scale @ 0x9d22260] TB:0.000001
[overlay @ 0x9d21200] main w:1366 h:768 fmt:yuv420p overlay x:1000 y:10 w:240 h:180 fmt:yuva420p
[overlay @ 0x9d21200] main_tb:1/3000000 overlay_tb:1/1000000 -> tb:1/3000000 exact:1
[libx264 @ 0x9d0ee20] VBV bufsize set but maxrate unspecified, ignored
[libx264 @ 0x9d0ee20] using SAR=1/1
[libx264 @ 0x9d0ee20] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle Cache64
[libx264 @ 0x9d0ee20] profile Main, level 3.2
Output #0, avi, to 'ScrVideo.avi':
  Metadata:
    ISFT            : Lavf53.21.1
    Stream #0.0: Video: libx264, yuv420p, 1366x768 [PAR 1:1 DAR 683:384], q=-1--1, 512 kb/s, 30 tbn, 30 tbc
    Stream #0.1: Audio: libvo_aacenc, 44100 Hz, 2 channels, s16, 96 kb/s
Stream mapping:
  Stream #0:0 -> #0:0 (rawvideo -> libx264)
  Stream #2:0 -> #0:1 (pcm_s16le -> libvo_aacenc)
Press ctrl-c to stop encoding
frame=  219 fps= 31 q=-1.0 Lsize=     179kB time=6.34 bitrate= 231.3kbits/s
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