In what ways was the Soviet Army effective in the Soviet-Afghan War? In what ways was it ineffective?

The Soviet Army was largely ineffective in Afghanistan. Granted, they did have small successes with Air-Assault formations and Special Forces.

I'll outline the Soviet Army's shortcomings with the following:

The Soviet Army of 1980 was trained and equipped for large scale, conventional warfare in Central Europe against a similar opponent. As such, the Soviets fought against the Mujahideen using their Armored and Motor-Rifle formations, which proved extremely ineffective against a small scale guerrilla enemy who used hit-and-run tactics in the rough terrain of Afghanistan. These large formations weren't mobile enough to engage small groups of Muj fighters that easily meshed back into the terrain.
The Russians used large scale offensives against Mujahideen strongholds, such as in the Panjshir Valley, which didn't really result in much, other than temporarily clearing those sectors. The biggest shortcoming here was the fact that once the Russians did engage the enemy in force, they failed to hold the ground by withdrawing once their operation was completed. Also, their practice of clearing territory, which entailed killing of civilians in addition to enemy combatants, resulted in a failure to actually defeat the enemy in the long term.
The Soviets didn't have enough men to properly occupy and pacify Afghanistan. The peak number of Soviet troops during the war was 115,000 in the 40th Army, which consisted of a mere 5 divisions. The bulk of these troops were conscripts, which led to poor combat performance in their Motor-Rifle Formations. However, the Russians did have their elite infantry units, such as the famed Spetsnaz, the VDV, and their recon infantry. The problem with their elite units was not combat effectiveness, but the fact that there were not enough of them and that they were employed incorrectly.
This point ties in with incorrect employment. Intelligence gathering is essential to a successful COIN campaign. The Soviets over-relied on aerial recon and radio intercepts while using their recon infantry and special forces in direct combat roles. This gave them very inaccurate intel reports. Although their special forces and recon inf, performed very well in combat against the Mujahideen, they would have better served in intelligence gathering.

Now as I mentioned earlier, the Soviets did have one effective method during the war. Their use of Air Assault (Helicopter-borne) infantry, such as the VDV, in conjunction with their ground forces, was very effective in assaulting Muj strongholds in the rough and mountainous terrain of Afghanistan. Helicopters could move fast and allowed for rapid insertion of infantry to encircle and destroy Muj forces. Likewise, the helicopter insertion of Spetsnaz teams to interdict and ambush Muj fighters was also effective.

Source: The Soviet-Afghan War 1979-89 by Gregory Fremont-Barnes.