This is what's been working for me.
For most switch chips except the newer CRS3XX series, you want to be closer to config 2.
Put all ports from the switch(s) directly under a single bridge.
Do NOT use the vlan section under bridges and leave VLAN filtering unchecked in the bridge options.
Add all needed management and routable VLANS under interfaces/vlans with the new bridge as the parent interface.
Set up your vlan tables and ports under /interfaces/switch with fallback,check or secure. Be sure to include the swtich_cpu ports with any VLANS needing management or routing.
Here's a working config from my RB2011 (acting as a switch) with multiple VLANS, trunked on Ether1 with others as access ports.
# dec/28/2017 15:28:05 by RouterOS 6.41
# software id = AD6T-JK3F
#
# model = 2011UAS
# serial number = XXXXXXXXXXXXXX
/interface ethernet
set [ find default-name=ether1 ] name=ether1-trunk
set [ find default-name=ether2 ] name=ether2-Cams
set [ find default-name=ether3 ] name=ether3-36Dog
set [ find default-name=ether4 ] name=ether4-Servers
set [ find default-name=ether5 ] name=ether5-CapMan
set [ find default-name=ether8 ] name=ether8-Cams
set [ find default-name=ether9 ] name=ether9-Servers
set [ find default-name=ether10 ] name=ether10-Management
/interface bridge
add admin-mac=XX:XX:6D:97:XX:XX auto-mac=no comment=defconf name=bridge \
protocol-mode=none
/interface vlan
add interface=bridge name=vlan99-Management vlan-id=99
/interface ethernet switch port
set 0 default-vlan-id=1 vlan-mode=secure
set 1 vlan-header=add-if-missing vlan-mode=secure
set 2 default-vlan-id=8 vlan-header=always-strip vlan-mode=secure
set 3 default-vlan-id=3 vlan-header=always-strip vlan-mode=secure
set 4 default-vlan-id=4 vlan-header=always-strip vlan-mode=secure
set 5 default-vlan-id=44 vlan-header=always-strip vlan-mode=secure
set 6 default-vlan-id=1 vlan-mode=secure
set 7 default-vlan-id=99 vlan-header=always-strip vlan-mode=secure
set 8 default-vlan-id=8 vlan-header=always-strip vlan-mode=secure
set 9 default-vlan-id=4 vlan-header=always-strip vlan-mode=secure
set 10 default-vlan-id=99 vlan-header=always-strip vlan-mode=secure
set 11 vlan-header=add-if-missing vlan-mode=secure
set 12 vlan-header=add-if-missing vlan-mode=secure
/interface list
add exclude=dynamic name=discover
add name=mactel
add name=mac-winbox
/interface bridge port
add bridge=bridge comment=defconf interface=ether2-Cams
add bridge=bridge comment=defconf interface=ether6
add bridge=bridge interface=sfp1
add bridge=bridge interface=ether1-trunk
add bridge=bridge interface=ether3-36Dog
add bridge=bridge interface=ether4-Servers
add bridge=bridge interface=ether5-CapMan
add bridge=bridge interface=ether7
add bridge=bridge interface=ether8-Cams
add bridge=bridge interface=ether9-Servers
add bridge=bridge interface=ether10-Management
/ip neighbor discovery-settings
set discover-interface-list=discover
/interface ethernet switch vlan
add independent-learning=no ports=ether1-trunk,switch1-cpu switch=switch1 \
vlan-id=99
add independent-learning=no ports=ether1-trunk,ether5-CapMan switch=switch1 \
vlan-id=44
add independent-learning=no ports=ether1-trunk,ether2-Cams,switch1-cpu \
switch=switch1 vlan-id=8
add ports=ether8-Cams,switch2-cpu switch=switch2 vlan-id=8
add independent-learning=no ports=ether1-trunk,ether3-36Dog switch=switch1 \
vlan-id=3
add independent-learning=no ports=ether1-trunk,ether4-Servers,switch1-cpu \
switch=switch1 vlan-id=4
add independent-learning=no ports=ether1-trunk switch=switch1 vlan-id=5
add ports=ether10-Management,switch2-cpu,ether7 switch=switch2 vlan-id=99
add ports=ether9-Servers,switch2-cpu switch=switch2 vlan-id=4
/interface list member
add interface=sfp1 list=discover
add interface=ether2-Cams list=discover
add interface=ether3-36Dog list=discover
add interface=ether4-Servers list=discover
add interface=ether5-CapMan list=discover
add interface=ether6 list=discover
add interface=ether7 list=discover
add interface=ether8-Cams list=discover
add interface=ether9-Servers list=discover
add interface=ether10-Management list=discover
add interface=bridge list=discover
add interface=vlan99-Management list=discover
add interface=bridge list=mactel
add interface=bridge list=mac-winbox
add list=mac-winbox
add interface=vlan99-Management list=mac-winbox
/ip dhcp-client
add dhcp-options=hostname,clientid disabled=no interface=vlan99-Management
/ip dns
set allow-remote-requests=yes
/ip firewall filter
add action=accept chain=input comment="defconf: accept ICMP" protocol=icmp
add action=accept chain=input comment="defconf: accept established,related" \
connection-state=established,related
add action=drop chain=forward comment=\
"defconf: drop all from WAN not DSTNATed" connection-nat-state=!dstnat \
connection-state=new disabled=yes in-interface=ether1-trunk
/system clock
set time-zone-name=America/Los_Angeles
/system identity
set name=RB2011
/system package update
set channel=bugfix
/tool mac-server
set allowed-interface-list=mactel
/tool mac-server mac-winbox
set allowed-interface-list=mac-winbox